Forces of Nature
by Devil Spice
Summary: The team go on an offworld recon mission and end up in a fight for Sheppard's life. Here's chap 24 for your enjoyment. And I think it kicks butt! I love it!
1. Chapter 1

I do not own any of the characters of Stargate Atlantis. This is entirely a work of fiction that came out of my head. Please read and tell me what you think. This is my first posting. Not my first fanfiction, just my first posting. This may be only chapter one but I have a lot more written. It's just not on my computer yet. I'm only part way through putting chapter two on my system. So bear with me please.

**Forces of Nature**

**By: Devil Spice**

**Chapter One**

Lt. Colonel John Sheppard came running into the Gate room at a dead run and out of breath.The others on his team turned at the commotion and were surprised to see that it was their CO. He was usually the first one at the gate waiting for the others to show up.

This was the first time that it had been the other way around. He looked like he had just woken up. His dark hair was even more disheveled than usual, his jacket and tactical vest were both undone and his P-90 was in his hand, not even attached to his vest yet. He also looked like he was extremely tired.

He stopped in front of the team breathing heavily, which was something else that was new. Most of the time he did not look like anything was bothering him if he had been running. He was a very fit person. A trifle thin, but still fit and athletic. A lot of people mistook him for somebody who wouldn't be able to fight. But those who knew him, who worked with him, knew that he was a fierce and determined fighter. Headstrong, extremely loyal to the extreme where he would die for those he loved and trusted. And beyond the levels of loyalty and fighting ability he was one of the most modest, mysterious and nice people anybody could meet.

He also had a wicked sense of humour. And was quite adept at sarcasm both in jest and when he really meant it. He was most definitely not someone who should be crossed. And those stupid enough to actually do so for the most part regretted it.

He calmed down his breathing and stood in front of Dr. Rodney McKay, Teyla Emeggan and Specialist Ronan Dex and slowly did up his jacket and tac vest. Almost non-challantly he finished getting ready. When he finally had his P-90 attached to his vest he looked at his team with that 'Are we ready to go yet' face.

"What took you so long Colonel Sheppard?" Teyla asked with a cock of her head.

"Sorry guys. I over slept." Was the only answer that John gave them. No reason beyond that. No reason that would make him slide from his routine.

They all looked at him with confused looks on their faces. They knew that he wasn't on his game. They knew that something was wrong with their CO. And they knew that he would never own up to any problems. Health or otherwise.

"Is everybody ready to go Colonel?" came a disembodied voice over the com system.

John turned and looked up at Dr. Elizabeth Weir who was just making her way to the control room. When she reached the balcony she looked down at SGA-1 and smiled.

"We're good to go Elizabeth." John said before anybody else could utter a word to the contrary.

Elizabeth turned back to the tech at the controls and told him to dial the planet that her team was going to for recon. Less than a minute later the bright blue flowing wormhole came to life and then shimmered in the gate.

"You have a go Colonel." Elizabeth said after she turned back to face them.

John nodded his head and then walked towards the event horizon. The other three lingered momentarily and then followed John through. Intent on keeping an eye on their CO. A very close eye. If John showed any signs of health issues or anything else they wanted to be ready for it.

**TBC in Chapter Two...**

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**Author's Note:** I don't know when I will be able to post chapter two, I can be a little slow when it comes to putting my stories onto my computer. But don't worry, I'll try as soon as I can. And as I said at the beginning... reviews are welcome (good or bad). They will help me keep perspective on my writing.


	2. Chapter 2

I do not own Stargate Atlantis. Not the show or any of it's characters (except for the villargers which I made up in this story - and my bad guy).

So here you go since you asked so nicely. Chapter two is up and running. I thank you soooo much for the reviews. I am a happy person that you liked my story so much. Now I only hope you like the rest. And there's plenty more to come. Have fun reading.

**Chapter Two**

When they stepped out of the event horizon onto the planet they had named P3J-448, they saw John standing by the DHD with is P-90 at the ready, waiting for the rest of his team to come through.

John turned when he heard them come through and smiled. "What took you guys so long?" he asked with that lop sided grin of his.

"You know us Sheppard," McKay said, "making sure we have everything we need before we go through."

"Well, now that we're all here we might as well go see what we can find, huh?" John turned and started to head off towards the forest. The others just looked at each other and then hurried off after their CO.

"What is going on here Teyla?" Rodney whispered. "Why is Sheppard acting so weird?"

"I do not know Dr. McKay. He is acting quite strange." Teyla said with a slight frown on her face.

"Strange is putting it mildly." McKay said.

Ronan just walked along quietly, keeping a keen eye on John who was a little ways in front of them. He didn't know what was wrong with this man who he had begun to trust with his own life. He'd never seen John so disheveled except when he had the flu or had been stuck in the infirmary. He also knew that John had a tendency to keep any illnesses or injuries to himself so that he wouldn't be a hindrance to his team. He was stubborn.

As they made their way through the large forest they listened for any out of the ordinary noises. Anything to tip them off that something was wrong.

After two hours of recon they finally came to an opening in the forest and saw what looked like ruins of some kind. McKay's eyes widened with absolute delight. "Holy crap!" McKay said.

He slowly moved forward and John reached his hand out and grabbed hold of the doctor's arm. "Wait a minute Rodney. Let Ronan and I do a check of the clearing and ruins first. We don't know what's out there."

"Fine. Fine. I'll wait here with Teyla while the two of you get to look at the ruins first."

John nodded, missing the sarcasm in Rodney's voice. Then he moved forward with Ronan in tow.

Rodney just stared after him with a surprised look on his face. Something was definitely wrong with Sheppard because normally he would have come back with his own sarcastic comment.

Rodney and Teyla watched as Sheppard and Ronan systematically checked the area.

John bent to look under a fallen chunk of ruin and then knelt there for a moment with his arm on his knee. He coughed and the others looked over at him. He stood up slowly and continued his search without noticing that his friends were watching him.

"Did he just cough Teyla?" Rodney asked with slight concern.

"Yes. He did Dr. McKay. I heard it too. There is something wrong with his health. And he is not willing to tell us it would seem."

"Typical Sheppard." Rodney said with a little bit of anger but concern still evident in his voice.

When the recon of the area was finished John and Ronan returned to where Rodney and Teyla waited to hear their findings. "Well Rodney. You're free to go and look at the ruins. Everything looks okay. Just keep an eye out for anything coming our way. We'll do the same." Rodney nodded and then moved towards the ruins that he so excitedly wanted to look over.

* * *

A little over an hour after Rodney had started, John and Ronan were on the northern edge of the clearing keeping watch when John cocked his head like he heard something and then slowly moved forward into the forest.

Ronan went to grab his arm and missed, catching air instead. "Sheppard. Where are you going?" John did not answer him. It was like he was in a trance.

Ronan turned back and looked at Teyla and Rodney. Teyla nodded and Ronan followed John into the forest. He caught up to the man and placed his hand on John's shoulder. "What's going on Sheppard?" John pulled out of Ronan's grasp and continued to walk, P90 dangling from the clip on his tac vest.

"Sheppard!" Ronan said trying to keep pace with his CO.

After walking about ten minutes Ronan finally made Sheppard stop walking. He firmly grabbed hold of John's upper right arm and pulled him around to face him. John immediately collapsed in to Ronan's arms. Ronan caught him before he hit the ground and held onto him. He set his friend down gently on the ground and knelt down beside him.

The man was sweating and felt extremely hot to the touch. He was quite sick and Ronan knew that he had to get John back to Atlantis. He opened John's eyes with his fingers and saw how vacant they were. He took the P90 off of John's vest and clipped it to his own belt. Then he grabbed hold of Sheppard's arm and pulled him up. He then bent over and pulled the Colonel over his shoulders. When he was able to stand up he had John firmly planted over his shoulders. He put one hand around John's left arm and one around his left leg. He kept a good hold on his friend and made his way back to the clearing where Rodney and Teyla were.

* * *

When he finally emerged into the clearing Teyla and Rodney dropped what they were doing and ran towards them. "What happened Ronan?" Teyla asked as they came upon the two men. They helped Ronan place John on the ground and then they all gathered around him.

"Sheppard was in some kind of a trance and when I stopped him from walking he collapsed in my arms."

"What do you mean he was in a trance?" Rodney asked as he knelt down beside the Colonel.

"He just continued to walk into the forest and every time I tried to stop him he just ignored me and continued to walk. I don't know what was happening to him."

"Well, we have to get him back to Atlantis. Now." Rodney said as he placed his hand on John's forehead and felt the heat radiating from him.

"That's just what I was thinking." Ronan said as he reached down to pick John up again.

Just as he took hold of John's arm a shot was fired from the tree line. The three team members ducked when more shots were fired. Ronan and Teyla held up their weapons and began to fire around them. They stopped when they realized they couldn't see anybody.

More shots were fired and they circled around their fallen comrade. Within minutes they saw a group of people come out of the bushes on all sides of them. There was no place to retreat to. Every exit point was covered by the enemy.

**TBC in Chapter Three...**

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**A/N: **Sorry to leave you all hanging, but that's what makes you want to come back for more. Enjoy. Hehehehe. (Like my evil little laugh?)


	3. Chapter 3

I don't own Stargate Atlantis at all. None of it. Not even the characters (boo hoo). Except the ones of my own making that is. Hey there. I'm loving the reviews. Thanks so much for the positive feedback. I think my ego loves you for it. So here is chapter three. Hope you like it as much as the rest. Hopefully I can keep my little fingers tapping away at my keyboard to pump out the rest of this story. But there's a lot there folks, so don't expect something every day. Have fun readers.

**Chapter Three**

Rodney knelt down beside Sheppard and took hold of his arm. He tried to shake him awake but nothing happened. "Wake up Sheppard! We have to get out of here! Come on!" he yelled.

As the group of people came closer to them they could tell that they were carrying what looked like staff weapons but soon realized that they weren't. They were wearing clothes and looked quite dirty. But they also looked like they knew what they were doing too. A group of four came up to them holding their weapons. Two men and two women who seemed to be in their early twenties.

"Strangers!" the oldest male said. "Where do you come from? Why have you desecrated our holy land?"

Ronan stepped forward to answer the man. "We are Atlanteans. We come from the City of the Ancients."

They looked at each other and then back at Ronan. And in turn they looked from one to the other of the rest of SGA-1. "You lie." The male said. "The Ancient City was lost."

"Yes. It was." Ronan said. "But we are from Atlantis. That is no lie. My name is Ronan Dex. This is Teyla Emmegan and Dr. Rodney McKay. And our fallen comrade is Lt. Colonel John Sheppard. We didn't mean to defile your holy place. We were only looking. We were curious about your world. We're trying to get to the Stargate to bring our comrade back to the doctors. He needs help. He's sick."

The four again looked at each other and then back at the Atlanteans. "You will come with us defilers." The male said. "We will take you to our leader. He must set eyes upon you before you are dealt with."

"But Ronan said that we didn't mean to do anything. We were curious. Why do we have to be dealt with?" Rodney said as he kept hold of John's arm. Trying to protect him.

"Take them." The male said to the group who had moved up behind Rodney and the others. They were grabbed from behind and when Rodney felt hands on his shoulders he wouldn't let go of Sheppard. Then his hands were yanked away from John and he was brought over to stand with Teyla and Ronan. Two men picked up John by his arms and began to drag him along behind them.

"Hey! Be careful with him." Rodney said indignantly.

"Move it." One of the women said as she pushed him to make him move.

Stripped of their weapons they began to walk in the direction that they were being herded. They kept looking behind them to see what they were doing with John.

* * *

Twenty minutes later they came into view of a village with huts and were looking around at the people that came out to greet them. They came to stop in front of a small hut and were shoved unceremoniously into it. Then John was dragged in and they dropped him on the dirt floor.

"Thanks for nothing!" Rodney yelled out as the villagers left.

They stood up and raced over to the Colonel. He was sweating and shivering at the same time. He was clearly sick. They just didn't know how the symptoms came on so quickly. He seemed relatively alright earlier. But then within hours he was unconscious and showing a lot of symptoms.

Teyla reached her hand out and placed it on John's hot forehead. He flinched at the touch but did not wake up. "We have to get him back to Atlantis." Teyla said as John coughed. "There is something more going on with him than just being ill."

"I agree with you Teyla." Ronan said as he moved over to stand beside her. "There is a reason he went into a trance." He bent down, put his arms under the Colonel and lifted him up. "Let's move him to a more comfortable place. He shouldn't be laying in the middle of the floor."

He walked over to the makeshift bed that sat in the corner of the hut and placed him gently on the bed. "Help me get his vest off Teyla." Ronan said as he pulled John up by the shoulders. Teyla knelt down and unzipped the tac vest and then pulled it off one arm and then the other. She placed it on the ground and then turned back to unzip his jacket. She took it off and placed it on top of the vest. He was wearing a black t-shirt that was soaked through with sweat. He was continuing to cough as time went by.

"Is there anything we can do here to help him?" Rodney asked as he moved in beside them.

"I don't think so McKay." Ronan said almost in a grunt. He was angry that these villagers were keeping them there and that they would not help Sheppard. Rodney and Teyla could tell how mad he was. And they felt sorry for the villagers. Especially if he were to become even more angry.

* * *

They kept an eye on Sheppard throughout the night. Each taking a turn to make sure John didn't get any worse. At two in the morning Ronan sat cross legged on the floor beside his CO. He was wide awake and cleaning John's P-90. He felt that when John was ready to fight again he would need a working weapon. And since Sheppard was the one who had shown him how to clean Earth weapons he knew what he was doing.

He looked over at his friend every time he moaned or coughed or made any kind of movement. He moved a hand over to John's chest and placed his palm there. He felt the rise and fall of it as he breathed. Then quite suddenly John's eyes opened up and it looked like he was frightened. His breathing sped up and he sat up.

"Sheppard? What's wrong?" Ronan asked with concern. He did not receive an answer. John just seemed to stare off into space with afreaked out look on his face. Then John stood up slowly and walked towards the entrance to the hut.

"Sheppard!" Ronan said as he, himself, stood up.

Then Teyla and Rodney woke up to the commotion. "What's happening?" Rodney asked as he stood.

"I don't know McKay." Ronan said as he moved to catch up with John. "You can't go out there Sheppard. There are guards. They'll hurt you." He said taking a hold of John's upper arm. John yanked his arm away and continued to walk towards the entrance. When he pushed back the flap two guards immediately turned and grabbed a hold of him.

"Hey. Where do you think you're going?" the older male said. John turned on them in an instant and decked them. Within seconds the guards were out cold on the ground.

"Where the hell did that come from?" Rodney said with surprise. "He never did that before!"

"No. He did not." Teyla said and rushed forward.

John continued to walk out into the darkness and the others followed him with a mixture of curiousness and worry. Scared that something was taking him over.

* * *

They followed him for ten minutes and then he stopped in front of a cave entrance. Ronan and Teyla stood on either side of their friend and Rodney stood beside Teyla. Both Ronan and Teyla looked at Sheppard.

"Where are you taking us Colonel Sheppard?" Teyla asked as she placed her hand on his shoulder.

"I don't think that he's taking 'us' anywhere Teyla." Ronan said. "I doubt that he even knows that we're here. He's being drawn somewhere. I think that whatever sickness he has, has triggered this. And I think it happened as soon as we set foot on this planet."

"It's got to be the ATA Gene." Rodney said as he looked back at the cave entrance.

"Why would the Ancient Gene do this to him?" Teyla asked.

"I don't know Teyla. But it's the only logical explanation."

"But you have the Gene Rodney. You are not in a trance." Teyla said as she turned to look at him.

"Yes. But mine is artificial. John's is one hundred percent original. We're only about a fraction of the way through understanding the ATA Gene. There are bound to be things that we don't know about what the Gene does to John. He's got the strongest version of it that we know of. Something strong must be emanating from whatever is in this cave. It's drawing him here for some reason. So let's continue to follow him. See where he takes us."

"McKay. We have no weapons." Ronan said. "How are we supposed to defend ourselves if something happens?"

"Come on Ronan. Stop being paranoid." Rodney said as he kept his eyes on the entrance to the cave.

Sheppard stepped forward and walked into the cave.

**TBC in Chapter Four...**

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**A/N: **Let me know if the chapters seem choppy to you. I didn't actually write this with chapters in mind. It's really one big, long, ongoing story. But I can't type the whole thing out at once. Remember, I wrote it in a book first. So it's pretty much going through my story and picking out what I think are the best spots to start a knew chapter. TTFN. And sorry for the cliffhanger again. Hehe. :)


	4. Chapter 4

I do not own Stargate Atlantis, the show or the Characters. But this story is one hundred percent original. Out of my freaky brain. Hey there folks. You know, you are the ones who got me to post chapter four. I wasn't going to type any chapters tonight, but I started and just had to finish the chapter. Yay! And whew, am I tired. Sitting here, sweating away (I don't think my Central A/C is working very well), listing to music and typing. Wow, I can do three things at one time... amazing. Anyways, thanks for the reviews. They're awesome. I can't believe you all like it that much. Thanx a bunch. Have fun reading. It's a longer chapter this time. Ta. :)

**Chapter Four**

They all followed John into the cave and Teyla pulled the flashlight out of her vest and turned it on. Rodney followed suit and turned on his as well.

John seemed to know exactly where he was going because he never once slowed down. He just continued on his path. They seemed to be going in to the depths of the cave and fifteen minutes later they spotted a glowing blue light that seemed to come from everywhere.

"That must be where we're headed." Rodney said.

When they turned the corner they seemed to be in a large chamber. The light was now almost overpowering. John still did not stop. He walked to the middle of the chamber and stopped in front of a crystalline structure that stood almost ten feet tall. He reached his hand out and placed it on the structure. Almost immediately it lit up and began to turn.

Ronan, Teyla and Rodney covered their ears as the noise got louder. It didn't seem to affect Sheppard. He just stood blankly staring at it. The light flared and the noise rose. Then suddenly a beam of light shone out from the top and then out of the cave into the night sky.

John reached out his hands and placed them on the light. He closed his eyes and he twitched almost imperceptibly. The others ran forward and reached out to pull him away from the structure. The moment they touched him they were thrown backwards by an electrical force. They landed with a thud on the ground and slowly sat up to look at Sheppard. He was still standing with his hands on the light.

"Okay. What the hell just happened?" Rodney said as he slowly stood up and rested his hands on his lower back.

"The Ancient Gene." Ronan said as he helped Teyla to her feet.

"Wow. That's some new trick he has." Rodney said as he moved towards the structure. He circled around so that he could see John's face. His eyes were still closed and his lips were moving but he wasn't saying anything. Rodney couldn't read his lips. "I think this thing is downloading information into his brain."

"Why do you say that Rodney?" Teyla asked as she moved over to stand beside him.

"Because his lips are moving. Look at them. We have to get him off this thing now."

* * *

Five minutes later John took his hands away and continued to stare into the light. Then before they knew it, John blinked and breathed in heavily. He looked around confusedly and then jerked when he saw Rodney, Teyla and Ronan looking at him.

"Rodney?" he said quietly.

Rodney reached out his hand to take hold of his friend and John collapsed into his arms. "Quick! Help me you guys!" he yelled out as he grabbed his friend before he hit the ground. Ronan and Teyla raced forward to help.

They were able to get him to the ground just as the villagers arrived at the entrance to the chamber. He lay on his stomach, arms sprawled out to the side and all three of his friends were beside him.

"What is going on here?" the leader said as he walked into the chamber.

The Atlanteans looked up and saw the villagers moving towards them. "We don't know." Rodney said. "We followed him here. Then all hell broke loose."

"Take them." The leader said.

"But what about that?" Rodney said pointing to the crystalline structure. It was still turning and flashing light. The beam was still shooting out of it.

"We have never seen it before. We did not know it was here until now."

"Well, that is Ancient." Rodney said. "And that is doing something that maybe we can help you with."

"What about him?" the leader said pointing at the unconscious Sheppard. "How did he know this was here?"

"He has the ATA Gene." Rodney said matter of factly.

"And what is that?" the leader asked.

"The Ancient Technology Activation Gene." Rodney said as if the leader was supposed to know what that was. Rodney sighed when he saw the confused look on the leader's face. "He's part Ancient. At least in the genes. Somehow he was able to start this thing up."

"What does it do?" the leader asked.

"That we don't know." Rodney said as he reached out and placed his hand on John's back. John convulsed after he was touched and then he was awake, breathing heavily.

"Rodney? Rodney! Are you there?" Sheppard said with fear in his voice.

"I'm here John. I'm here. Don't worry my friend. We're all here for you. Teyla, me and Ronan."

"Where am I?" he coughed and tried to sit up.

"Stay down Sheppard." Ronan said, placing his hand on John's back. "You're not well."

"Ronan? Where am I?"

"Just calm down Sheppard. We're on P3J-448." Ronan said.

They rolled him over slowly and saw the fear in his eyes. He had no clue where he was. No clue at all. He was beginning to hyperventilate. "I want up Ronan. I want up."

Ronan nodded and then reached out to help him to his feet. Rodney jumped forward to help too. John swayed momentarily when he reached his feet and then steadied himself. Ronan and Rodney kept hold of him.

"Woah there Sheppard." Rodney said. "We don't want you falling again."

John looked up at the structure and creased his brow. "What is that?"

"Um. We don't know. We were kind of hoping you could tell us." Rodney said following his gaze.

The structure flashed red momentarily and John grabbed his head in pain.

"What's wrong Sheppard?" Rodney asked.

It flashed red again and John screamed, grabbing his head.

"It's that damn thing! Every time it flashes red it hurts him! What's it doing?" Rodney said as he tried to speak over the noise.

"We must get him out of here." Teyla said taking hold of John's hand.

"I don't think that's going to help Teyla." Rodney said.

"Why do you say that?"

"Just trust me on that Teyla. Trust me."

They grabbed hold of him and pulled him towards the entrance. John began to lose control. He began to yell. "NO! Where are you taking me? I want to stay here! I want to stay here!"

"John. What are you talking about? Rodney asked. "It's hurting you."

"NO! It's helping me! It's helping me!" John pulled out of their grasps and began to run back to the crystalline structure.

Ronan grabbed his arm and yanked him back. "Sheppard! You need to leave."

"Let go of me! Let go! It needs me!"

Ronan kept his grip on John's arm and forcibly pulled him to the entrance of the chamber. The villagers were watching all of this with surprise. Unsure of what to do they just let the team leave ahead of them. John was screaming the whole way.

By the time they reached the outside of the cave John's wrist was red from trying to struggle out of Ronan's grasp. The light turned red again and John yelled out in pain. He dropped to the ground and Ronan let go of him. John tried to run away back into the cave and Ronan grabbed hold of him around the chest. "Sheppard! You can't go back in there. It's not safe for you." He kept hold of John when he continued to try to get away. His arms and legs flailed.

"We have to get him back to Atlantis before this gets out of hand." Rodney said as he jumped forward to help Ronan with John. He took John's wrists in his hands and tried to hold them down against Ronan. John was a lot stronger than Rodney gave him credit for.

They dragged him back to the village against his will and were forced to tie him down to one of the beds, hands and feet, so he would not take off back to the structure.

He struggled constantly while the others were forced to watch him. His wrists were beginning to bleed from the force he was using to pull on the restraints. And he wouldn't stop yelling.

"Is there anything we can use to knock him out?" Rodney asked with major concern. Ronan, Teyla and the leader looked confused. "You know. Put him to sleep." Rodney said with some exasperation.

"Ah." The leader said. "Yes. I will get you something." He left the hut in hurry. Five minutes later he returned with a bowl of clear liquid.

"What is it?" Teyla asked.

"It is called Keehal. It, as you put it, knocks people out. It helps people to sleep."

"Great. Let's give it to him. I can't stand hearing him scream like that." Rodney said as he ran forward to take the liquid.

"I will give it to him. You do not know how much to give him."

"Okay. You can try. But I don't think he's going to let you. Ronan should be the one doing it. Ronan knows how to handle John. Trust me."

The leader nodded and handed the bowl to Rodney. Rodney in turn handed the bowl to Ronan. "How much do we give him?" he asked.

"A little over half of the bowl." The leader said, moving closer.

"Got that Ronan?"

Ronan nodded and turned towards Sheppard. The man was struggling so much that Ronan had to take hold of John's hair and force his head back. He took the bowl and placed it on John's lips. He poured what he could down in to his mouth and then held it shut with his hand. He put the bowl down on the floor and then made him swallow the liquid. It may not have looked right to the others, but Ronan knew it was the right thing to do. Minutes later Sheppard was out cold. No longer struggling, no longer yelling. Asleep.

"Wow. That stuff sure works quickly." Rodney said with shock in his voice.

"It is very powerful. That is why we use it. It is made from a plant that grows around here."

Ronan placed his hand on the Colonel's chest and felt that he was breathing calmly.

"How long will he sleep for… um… sorry. I don't even know your name." Rodney said as he walked over to check on John.

"My name is Official Lotal. And he shall sleep for the rest of the night."

"That's good." Rodney said. "But then he'll go all psycho Sheppard on us again when he wakes up."

"Maybe by then we will have found a way to stop the Ancient Device." Teyla said as she knelt down beside John and placed her hand on his cheek.

"Maybe." Rodney said. "But now that I think about it. I'm pretty sure that it was talking to him. Because he wanted to leave. Then that thing started to turn red and he changed his mind. It's telling him what to do. I think it felt him the moment he set foot on this planet. It felt that ATA Gene. That big, pulsing ATA Gene and it drew him in hook, line and sinker. Got him to turn it on. And now it wants to keep him here. Like he's a battery."

The others just listened to Rodney rant, only understanding part of it.

"What's a battery McKay?" Ronan asked curiously.

"Portable power." Rodney pulled his flashlight out and opened it up. "This is a battery." He said as he held up the tiny object. "This makes the flashlight work. See. Without it , no power. With it…"

The others nodded their understanding.

"This is what Sheppard is to that thing. Power. He keeps it going."

"Then we must get him back through the Stargate before it has complete hold of him." Teyla said. "We cannot let this happen."

"I agree Teyla. But how are we supposed to break the connection?" Rodney said trying to come up with something. "Listen." He said turning to Lotan. "Can we have some of our stuff back?"

"What do you require?" the man asked.

"My data pad and some of my other instruments." Lotan looked confused. "I'll show you. It's not weapons. I assure you."

Lotan nodded and then led him to the hut where all their equipment was stored. Rodney grabbed his data pad and life signs detector. Then he took a few of the other instruments and headed back towards the hut where the others were. When he arrived he immediately began to work on how to shut the Ancient Device down. His brain was working on overtime to help the Colonel out. He didn't deserve to be used that way. Not by a person and not by a machine. Definitely not by a machine.

"We should leave McKay to do his work." Ronan said as he watched Rodney type away on his data pad.

"I agree with you Ronan." Teyla said. "Let us leave him alone so that he can think."

Ronan nodded and then turned back to Rodney. "We'll leave you in peace McKay."

"Yes. Yes. Go away." Rodney said without looking up from the screen and flicking his hand in a dismissive gesture at them.

Ronan grunted at him and then turned and walked out the entrance. Teyla and Lotan followed him out. When they were outside Lotan turned to face them. "Is he always that way?"

"Unfortunately, yes." Ronan said. "But he'll keep an eye on Sheppard. He'll let us know if the Device is affecting him in any way."

"Then let us go get something to eat. And we will bring something back for Dr. McKay to eat as well."

"That sounds great Lotan." Teyla said as they walked to the main area of the village.

* * *

Back in John's hut he was sleeping peacefully. Rodney was going crazy as he continued to work out a way to help John. Then quite suddenly he looked up at Sheppard and walked over to him.

"How did this happen to you Sheppard? That damn ATA Gene. It screws with you so much. You would be so much better off without it. And this thing. It's going to use you up and then spit you out. We shouldn't have come to this planet. There was something wrong with you when you left and we just made things worse by coming here." He put his hand on the pilot's arm and there was an immediate reaction. John's eyes flew open and he began to speak in Ancient.

"Woah. That's new." Rodney said and grabbed his digital recorder so that he could catch what Sheppard was saying. Almost five minutes later he stopped and stared at the ceiling.

Rodney turned off the recorder and grabbed his radio. "Uh… guys. We have a situation here. Sheppard just woke up and started speaking in Ancient. And as we all know… Sheppard does _not_ speak Ancient."

"We will be there momentarily." Teyla said over the radio.

Rodney took the digital recorder and hooked it up to his data pad. By the time he had it running through the translator, Teyla, Ronan and Lotan were back in the tent.

"Have you figured out what he said McKay?" Ronan asked as he walked over to Sheppard and sat down beside him.

"Well, if you give me a minute I'll let you know if the translation program worked on the recording." Rodney said as he continued to type away. They all watched with baited breath to find out what John had said in Ancient.

The hut was quiet. Then finally, Rodney made a triumphant noise with his mouth. "I've got it. Listen to this." They listened to the artificial voice coming from the pad. "I am Puren. I am Supreme. You will all bow before me. And I will use this vessel to spread my word. This vessel is strong and carries the Gene of the Ancients. He will feed me. He will help me live. Bow before Puren. Bow before the Supreme."

**TBC in Chapter Five…**

* * *

**A/N:** Ugh. Another cliffhanger. Sorry, but that was just the best place to end the chapter. Let me know if you spot any spelling mistakes please. I've been pretty good, but I don't have anyone to read over this for me... except you guys that is. More chapters to come. Enjoy, enjoy, enjoy! TTFN. :)


	5. Chapter 5

I don't own Stargate Atlantis or any of it's characters. I do however own this story. Hey there folks. Sorry it's been a bit since I have posted, but it's been quite hectic around here. I'm planning my vacation. Woohoo! And it's about time to. But I thought that since I'm leaving later this week I would post a chapter or two to keep you going. I have chapter five and six on the computer now so you won't have to wait long for the next chap. Have fun readers. I'll make more notes when I post chapter six.

**Chapter Five**

"Well isn't that just peachy keen." Rodney said with a huff. "We're supposed to bow to our new god are we? Huh."

"We must sever the connection between Colonel Sheppard and the Device now." Teyla said as she moved in beside Ronan to sit by John.

"Easier said than done Teyla." Rodney said with some anger in his voice.

"Then we must come up with a plan." Teyla said, also feeling angry.

John coughed and they all turned to look at him. He was still staring at the ceiling. Then suddenly, he began to cough more and his eyes blinked in rapid succession. He sucked in a breath and then looked around confused as to where he was. He tried to move his hands up to his face and began to freak out when he realized he could not move them from off of the bed.

"Sheppard?" Ronan asked as he reached his hand out and placed it on his friend's arm.

John flinched at the touch but knew who it was. "Ronan? Is that you?"

"Yes Sheppard. We're all still with you. Teyla is here beside me and McKay is behind us working on his data pad."

"Why can't I move my arms from off of the bed?"

"We had to restrain you Colonel Sheppard. You were acting irrationally and we did not want you to hurt yourself or anybody else." Teyla said as she too reached her hand out and placed it in John's hand. She closed it around his and squeezed gently.

"What?" John said with a scared look. "Restrain me? What?"

"It is okay Colonel. Do not worry." Teyla said. "We are going to help you."

He was beginning to hyperventilate. They could see the fear building up within him and the three of them stood around him to try and comfort him.

"Calm down Sheppard, calm down. C'mon buddy. We're not going anywhere." Rodney said.

"Rodney? Is that you?" John asked trying to keep his breathing under control.

"I'm here." He said moving around the bed so that John could see him. John nodded his head slightly and then unconsciously pulled on the restraints, hands closing into fists slowly. His wrists were raw from all of the pulling he had done previously.

"Le me out please. Please. It hurts. It really does." He asked, in a bit of a childlike whine. The others had not heard him talk this way before. It was a bit worrying to all of them. He began to pull a little harder on the restraints, unaware that he was hurting himself more.

"John. Your are pulling to hard on your restraints. You are hurting your wrists." Teyla said as she and Ronan tried to hold his arms down to the bed.

"No. No. Let go. I need to get free. I need to. Let me go!" John said as he pulled on the restraints harder and tried to buck their hands off. He was starting to act strange again.

"You're being controlled Sheppard." Ronan said matter of factly. "We can't let you go. You'll go back to the cave."

John suddenly sat up as much as the restraints would allow, a look of pure hatred and anger on his face and yelled at them. "Free me now! Free me or you will all die! I command you! Free me!"

The team jumped in shock and surprise and stood staring at him. Ronan was the least affected by the reaction that John had. He grabbed hold of John's shoulders and pushed him down on the bed forcefully. "We won't let you go Sheppard. Don't think that threats will work on us. You'll stay where you are."

Sheppard's head cocked slowly and his mouth twitched in anger. "Would you like this body to perish Ronan Dex?" John said slowly and directly. "I can do that. And I will if you do not let me go. I will kill Colonel Sheppard. And there will be nothing that you can do."

Teyla and Rodney's eyes widened at the statement. Ronan just stared at Colonel Sheppard. Stared directly into his eyes as he bent over him, holding his shoulders down to the bed. "I told you I don't take threats well." Ronan said. Seconds later John's eyes fluttered shut and he began to convulse.

"Ronan!" Teyla yelled out.

The three reached out to try and help him. The convulsions stopped and John's body fell limp. McKay reached a hand out and placed it on his neck. "His pulse was ragged before." he said. "But now it's non existent! Help him now!"

Ronan began to do compressions on John's chest and then breathed into his mouth. He finished three sets and then suddenly Sheppard began to breathe by taking a huge breath. His eyes opened and he was breathing normally. Ronan left his hands on Sheppard's chest and looked into his eyes. Rodney and Teyla just stood, breathing heavily, eyes wide.

"I told you I could kill him." John said quietly.

"Yes you did Sheppard. Or should I say Puren?" Ronan said with a bit of a growl to his voice. "You _have_ been in control of Sheppard the whole time. We won't let you go. Kill him if you have to… but you need him to survive. You need his Ancient Gene. If you kill him you don't have your power source anymore. So I don't think you will. Not today. Am I right?"

A sly smile formed on the Colonel's lips and he looked from Ronan to Teyla to Rodney. "Good for you Ronan Dex. You are very perceptive. I do need Colonel Sheppard to keep me alive."

"Is the Colonel still alive Puren?" Rodney asked. "And I don't mean his body. Is he still in there somewhere?"

"Worried about your friend Rodney McKay?" Puren asked, looking at him.

"Yes I am worried. Extremely worried. I don't want him to die."

"What a friend you are Rodney McKay. You don't want to see your friend die." Rodney just stood and looked at John. He wondered how John could survive with that thing taking over his mind. They had to disconnect him soon or they were going to lose him forever. Body and mind. And that did not sit well with him at all. Sheppard had to live. He just had to.

"What? No snide comeback? I'm disappointed in you Rodney McKay. From what I can tell from Colonel Sheppard's mind, you are practically the sarcasm king. Between the two of you, you could both share the title."

"Just call me King Rodney." He said with a frown. He continued to stare at him. He

wasn't going to let Puren win. Not at Sheppard's expense. He moved away from the bed and went back to his data pad. He was bound and determined to help Sheppard any way he could. Even if that meant risking his own life. John had risked his life on more than one occasion for Rodney, so turnabout was fair play. It was his turn to work for John. But he wasn't going to let Puren see what he was thinking about. He wasn't going to let his plan be known. Not even Teyla and Ronan. It was going to be his plan. And it was going to be a good one.

**TBC in Chapter Six…**

* * *

**A/N:** Sorry this is a short chapter. It was a good ending. But don't fret, chapter six is a good sized one. And this chap isn't really a cliff hanger this time. Have fun. Ta.


	6. Chapter 6

I don't own Stargate Atlantis or any of it's characters. My story idea though. And the villagers and bad guy are mine. So here is chapter six folks. I was telling the truth. Huh. Surprise, surprise. I don't know when I'll be able to post next though. I don't know if I'll have internet or Microsoft Word where I'm going. You might have to wait until after I get back. Oh darn. I will be taking my story with me however. I'll be adding more to it. I do have a six and a half hour bus ride ahead of me people. Plenty of time to come up with more ideas for other chapters. So have fun and if I don't post anything over the next ten days or so, don't worry, I'm not dead. I'll be back.

**Chapter Six**

As the night moved into day the rest of SGA-1 tried to come up with a plan to help Colonel Sheppard. After several hours they had come up with nothing that would work without getting John killed. They had thrown each plan out the moment that they had come to the conclusion that Sheppard would die before they could sever the connection.

Rodney's mind was working furiously to come up with a working plan that would not involve the death of Sheppard.

John in the meantime, over the course of the remaining evening, had stayed awake. Puren had not spoken again, but they knew that he was alive and well within the Colonel's mind and John had been pushed to the recesses of his consciousness.

So the team had moved to another area of the village so Puren would not hear their plans. They had left one of Lotan's men inside the hut so that he could keep an eye on John and Puren. Things had been quiet inside the hut. So when Rodney had returned to check on him he was not surprised to see the villager sitting in the corner reading. John was staring at the ceiling, eyes not blinking.

Rodney nodded at the man in the corner and then walked over to Sheppard and sat down beside him. "Hey there Sheppard. Or should I say Puren? How's life treatin' you? You comfortable?" he said with a remark of sarcasm.

John did not answer. He sat staring at the ceiling. Not moving at all. It seemed like he was in a trance of some kind. Rodney suspected that Puren was keeping a tight leash on him. Keeping him under control so that the soldier would not get away.

"Okay. So don't answer me. See if I care. But I know it's not Sheppard in there. You may look like him, but you're not him." He reached out a hand and placed it hesitantly on John's shoulder. He still didn't move. Rodney knew that Puren was listening to everything that he was saying.

He kept his hand on John's shoulder trying to let him know that he was there. Even if he was way back, completely way back, in his mind. He knew that John was listening from somewhere. Listening to everything his friends had to say. Watching them try to help him and powerless to do anything about it. Powerless to say anything.

Teyla and Ronan walked in at that moment and spotted Rodney trying to get through to the Colonel. They walked over and stood on either side of him. They both placed a hand on one of Rodney's shoulders. Rodney flinched and looked back at his friends.

"Hey there. Puren is holding on to him pretty tight. He won't say anything and he won't move." Rodney stood up and turned around to face his two friends. "This totally sucks." He said and walked past them. "We don't have a plan. We don't have a way to save the Colonel. Puren is just going to keep on controlling him and may even hurt him physically. He's hurting him mentally, but the physical part may still be coming. That damn ATA Gene is going to be the death of him somewhere along the way. Everybody always wants him for the gene. At least this time it's not the Wraith after him." Teyla and Ronan just sat and listened to Rodney rant with smiles on their faces. He seemed to go on forever. When he finally did stop he noticed that they were looking at him.

"What?" Rodney said with a curious look on his face.

"Nothing." Ronan said and uncrossed his arms. He shook his head and turned to look at John. He bent down and placed his hand on Sheppard's forehead. "He has a fever I think." He said as he sat down.

Teyla made her way over to them and felt his forehead for herself. "He does have a fever." She said. "Puren is hurting him physically like you said Rodney. His body can't take much more of this. I think he will burn out. Like Rodney said, he is being used as power. And the more energy that is taken away from him the sicker he will become."

They walked over to the entrance to the hut and watched the beam continue to shoot out from the mountain. Ronan leaned against the door and crossed his arms. Teyla stood just outside the door, hands on her hips. Rodney stood at the other side of the door, feet apart and arms crossed in front of him. Not a word was said between the three for what seemed like an eternity. They just stood and watched, thinking as hard as they could about any plan at all.

"Is it me, or does the beam look like it's slowing down a bit?" Rodney said as he moved outside of the hut. Teyla and Ronan looked a little closer trying to see what Rodney had seen.

"You know, I think he's right." Ronan said. "It's getting slower."

All three turned and looked back at John. His eyes were blinking and his breathing was quite heavy. They ran back in and raced to his side. "Colonel?" Teyla said, placing her hand on his arm.

John coughed and tried to sit up. When he was hampered by the restraints he was forced back onto the bed. "Where am I? What's going on?" John said with fear in his voice. They could tell this time that it was John they were talking to and not Puren.

"For some reason Puren has left John." Rodney said. "Maybe it's resting."

Again John spoke up. "Where am I? I don't understand what's happening." He balled his hands into fists and began to pull on the restraints again. They didn't think that he realized what he was doing. He coughed again.

"It's okay Colonel." Teyla said keeping a grip on his arm. "We are here. We are not going to let anything happen to you."

"Teyla? I can feel something reaching into my mind. I don't know what it is, but it's trying to tell me something."

"Don't listen to it Sheppard." Rodney said. "Listen to us. Listen to your friends." He knelt down and placed his hands on John's cheeks to force him to look at him "Don't pay attention to what Puren has to say. He's evil and he's using you."

John just looked into Rodney's eyes and began to shiver. He nodded his head slowly, eyes wide as saucers and said "Okay." He pulled on his restraints again and they could see the bruising and chafing from all of the pulling. It wasn't bad with his ankles because he was still wearing his boots and pants. The restraints were strapped over the ankles of his pants. "Help me please." John said in a small voice as a few tears began to form in his eyes. They had not seen him like this. It was a bit frightening and sad to see. Puren had slipped away, probably resting for the final battle. At least that's what they were calling it.

Rodney took his right hand and slowly moved over the top of John's head. His fingers moving through his dark, spiky hair. "It's okay Sheppard. Really. But we can't release you. Puren could come back and take you over again."

Sheppard closed his eyes in frustration and then opened them again. He looked into Rodney's eyes again and tears slid down his dirty cheeks. He sniffed and then turned his head to the side. Rodney's hands slipped off of his head. He looked sadly at his friend and then placed his hand on John's head again. Softly patting the side of it and then he stood up beside Teyla and Ronan. He noticed that Teyla also had tears in her eyes.

Ronan just stood with his arms crossed, feet apart and a frown on his face. He did not like what this thing was doing to Sheppard and the look on his face proved that.

John just seemed to give up and lay there with his head to the side, tears streaming from his eyes. Rodney turned suddenly and stormed out of the hut. Teyla and Ronan took off after him, leaving the villager to stay with John.

"What are you doing McKay?" Ronan asked as he caught up to the physicist.

"I'm going to tell that thing off. That's what I'm going to do. Or I'm going to blow it up! I don't care. I'm just going to get it out of Sheppard once and for all. I'm not going to let that thing kill my friend!"

"We don't have a plan McKay." Ronan said as he grabbed hold of Rodney's wrist.

"I don't care!" Rodney said as he yanked his wrist out of Ronan's hand and continued to speed walk towards the mountain where Puren sat.

Ronan and Teyla just followed him knowing very well that Rodney was extremely mad. So mad that he was willing to do anything to help free the Colonel from the grasp of the Ancient Device.

* * *

When they finally reached the inner chamber of the cave they saw that the crystalline structure of Puren was turning a lot slower than it had before and the beam was not as bright as it previously was.

"Hey Puren! You son of a bitch!" Rodney yelled out. "Wake up you bastard! I want to talk to you!" The three stood side by side in front of Puren with their arms crossed. There was no answer. "Hey! I'm talking to you!" Rodney yelled out.

Puren flashed red and then finally answered him. "What do you want Dr. Rodney McKay? Why have you woken me?" came a voice they had not heard before. The real voice of Puren. It bellowed through out the chamber and it sounded artificial.

"There you are." Rodney said with anger in his voice. "It's about time you decided to show yourself. For real I mean."

"Why have you woken me?" Puren spoke out again before Rodney could finish what he was saying.

"Yes, yes. I'm getting to that. Hold your damn horses will you." Rodney moved even closer to Puren and stood with his hands on his hips. He looked straight at the structure, sighed and began his tirade. "I think it's about time that you let go of Colonel Sheppard. And if you don't the three of us, along with the whole of Atlantis will kick your ass. Although I don't think that you have an ass per se. So we'll probably just blow you up. What do you say to that Puren? Huh? What do you say to that?"

"What do you mean the whole of Atlantis? The Great City is no more. You are not Lanteans. You do not possess the gene. Colonel Sheppard is the only one who possesses the real gene. Yours is artificial Dr. Rodney McKay. His is natural."

"I thought you knew everything about us from reading Sheppard's mind?" Rodney said as he changed his stance slightly.

"Colonel Sheppard is very adept at keeping parts of his mind from me. He has built up a wall around certain information. You lie. You are not Lantean."

"Yeah. Okay. Whatever you say Puren." Rodney said with sarcasm. He shook his head with frustration. "You just don't understand do you?" he said. "We are quite capable of kicking your ass. Just because you don't believe me, that isn't my fault."

No answer came back to them for at least a couple of minutes. "I will make Colonel Sheppard tell me what I wish to know."

"You do that," Rodney said, "and we will most definitely blow you up. You hurt him in any way and you're dead meat my friend."

Ronan and Teyla moved up beside Rodney and stood on either side of him with their arms crossed, reinforcing what Rodney had to say. All three had looks of pure hate on their faces. Ronan's was most evident.

Again there was silence. From both sides. Then Puren broke the silence. "I believe that Colonel Sheppard is Lantean. You however, I do not believe are Lantean. He carries the gene. From reading Colonel Sheppard's mind I understand that you have many weapons. So I do believe that you can harm me."

"Well there you go." Rodney said with a large sigh. "He finally understands where I'm coming from."

"Will he let go of Sheppard?" Ronan asked with a grunt.

"Yeah. So how about it Puren? Are you going to let our friend go now that you know what we are capable of?" Rodney asked, the anger still evident in his voice.

"I will let him go because I fear my end. I have just been woken up. I have no desire to die now. But be cautious. I have great power. You do not know everything that I am capable of either."

"Understood." Rodney said. "Now do what you said and let Sheppard go."

Puren turned red once more and then turned a shade of blue. That lasted a couple of minutes before Puren answered again. "It is done."

"How do we know that for sure?" Rodney said with some skepticism. "You could just be playing with us. You did it before when you made us think that you were Sheppard."

"You must trust me."

"Hmm." Rodney sniffed. "Trust you. I don't think so. Not after what you did to Sheppard."

"If you wish. But I have taken my presence out of his mind. You are free to do with him as you wish."

"Yeah. I'll believe that when I see it." Rodney said and then turned to leave the chamber.

"You do best to take him away from here Dr. Rodney McKay." Puren said with a voice that seemed even louder than before.

Rodney turned to face the structure. "Well duh." He said sarcastically and turned to leave again. Teyla and Rodney followed after him.

They made their way back to the hut where John lay restrained. When they arrived back they saw him wide awake, his head still facing towards the entrance. Depression covered his face.

Rodney reached forward and placed his hand on John's cheek again. "Sheppard? We're going back to Atlantis now." He said quietly. "Are you there?" John looked up slowly at Rodney and his eyes looked heavy. Like he was sad throughout his entire body. Which probably wasn't far from the truth. "Hey there buddy. Are you okay?"

"Can I go home now Rodney?" he asked in a tiny voice. One they had never heard come from his mouth before. He sounded like a child and it was extremely scary to hear that. Rodney brought his other hand up and placed it on his friend's arm. "Yeah. We can go home now. We'll make things better." John sniffed, suppressed a cough and then passed out with Rodney still holding onto him.

"What happened?" Teyla asked as she and Ronan raced forward.

"He's exhausted. And he's getting sicker." Rodney said as he sat down beside the man.

"Then let's go to Lotan and ask to bring him back to Atlantis." Teyla said as she began to head out of the hut.

"Wait!" Rodney said. Teyla stopped and turned to face her teammate. "There has to be a way that we can find out if Puren has left him or not."

"How do you propose to do that McKay?" Ronan asked.

"What am I? The answer man? Am I supposed to come up with all of the answers." Rodney said with some frustrated attitude. Both Teyla and Ronan gave him looks that he could read quite well. "Sorry." He apologized. "You know me and desperate situations."

The two nodded but kept the looks firmly planted on their faces. Rodney looked away and back at John. He didn't know how to figure out if Puren had left his friend's mind or not.

"I do not think that there is a way Rodney." Teyla said. "We must take a risk and bring him back to Atlantis."

"We have to take precautions when we go back." Ronan said. "We'll see what we can come up with."

Rodney sighed, knowing that both of them were right. There was no real way to tell. If Puren was still in him then he would show himself, 'itself', eventually. Then they would know to go back to P3J-448 and blow the hell out of Puren.

"Okay. Then let's go talk to Lotan. I think he'll understand where we're coming from." Rodney said. The three left the villager to look after John and then headed of to find Lotan.

* * *

Less than two hours later they were gathered at the Stargate, waiting to bring John through. They had Sheppard laying on a makeshift stretcher on the ground. Rodney stood at one end of him while Ronan stood at the other. Teyla was at the DHD with Lotan and another villager.

"I thank you Lotan." Teyla said. "_We_ thank you. For letting us take Colonel Sheppard home. I only wish we could help you with Puren. He is awake now and he is dangerous. He may come after you."

Lotan smiled at Teyla, took her hand and cupped it in both of his hands. "We only hope that you are able to help Colonel Sheppard get better. Now that we have gotten to know you, we realize that you are great people. You are loyal to each other and you have been nothing but nice to us. And don't worry about Puren. We will not enter into his mountain. We will stay in our village. We do not wish any confrontation."

Teyla smiled back and then took her free hand and patted his. "Thank you so much for your help." She said sweetly.

"Um… sorry to interrupt your schmooze fest Teyla," came Rodney's voice from where he stood with Ronan and John, "but can you get on with it? I'd like to get back to Atlantis before I grow old."

She gave the man a harsh look and then turned back to Lotan. "Sorry for Rodney's rudeness Lotan. He does not deal with stress very well."

"It's okay. I understand that he wishes to get home."

They let go of each other's hands and Teyla began to enter the address for Atlantis. When she finished she entered her IDC and then moved over to stand with her team. She watched as Ronan and Rodney went through the event horizon with John and then turned to wave at Lotan and the other villager. Then she too went through the gate that would take her back home.

**TBC in Chapter Seven…**

* * *

**A/N: **Well there folks. Can you guess what's going to happen next? They're going to Atlantis obviously. But after that? Let me know if you have any ideas on what is going to happen next and I'll see how close you are because I do have a lot more already written. If I don't write any of you back, don't worry. It just means that I probably don't have the internet where I am. Bye for now. I'm going to be the happy vacationer. Later days folks. TTFN.


	7. Chapter 7

I don't own Stargate Atlantis or any of it's characters. Except for the few that I have made up myself.

Hey there folks. It's been awhile. Sorry for the long wait between chapters. I'm back from my vacation and I had an awesome time. Feels weird being back at work. And now I've been able type out another chapter. Hope you like this one. I didn't get to write a whole lot while I was away, traveling too much, but that's okay because I still have a bunch written that I can post. Have fun reading folks. I look forward to the reviews.

**Chapter Seven**

When the gate activated in Atlantis, Dr. Weir made her way as fast as she could to the Control Room. She had been waiting for word from Colonel Sheppard's team. They were overdue and she had no idea why. She knew that something had gone wrong. That was the only reason why there would have been no contact from SGA-1. "Is there any IDC?" she asked the technician at the main console.

"It's coming through now Dr. Weir." He said. "It's Teyla's."

"Deactivate the shield and get Dr. Becket here immediately." She said hurriedly. He did as he was told and they waited to see their number one team come through the gate.

Less than two minutes later they saw Ronan pass through the event horizon and then Rodney. They were carrying something between them. Everyone was shocked to see that it was Colonel Sheppard. Less than a minute later Teyla come through and she turned to face the gate. She watched as the wormhole disengaged and then moved towards the rest of her team.

They were all bent down beside John when Weir came running down the stairs and Dr. Becket entered with a couple of nurses on his heal with a gurney. Dr. Weir looked at the state of her team and crouched down beside them. "What happened?" All four of them looked quite dirty and exhausted. John was unconscious and had several cuts on his face. But none looked too deep.

"There is an Ancient device on that planet." Rodney spoke up first. "It felt Sheppard when he arrived on the planet and took control of him. It made him wake it up and then it completely took him over. We had to restrain him so that he wouldn't go back and feed it more power."

"How were you able to get him back here if this thing took him over?" she asked.

"It was McKay." Ronan said. "He got so mad at it that he told it we would blow it up if it didn't let Sheppard go. That we would bring back people from Atlantis and kill it."

"Is that a hint of admiration I hear in your voice Ronan?" Rodney asked with a smirk. Ronan grunted and turned his attention back to Elizabeth.

"Lotan, the leader of the village where we were, helped us get Sheppard back to the gate. I think that we have a new ally with these people."

"That's great news." Weir said as she stood when Becket and Ronan put John on the stretcher. They began to wheel him to the infirmary with Teyla, Ronan, Rodney and Elizabeth close on their heels.

* * *

Arriving at the infirmary they got the Colonel onto a bed and stripped him down to his black boxer shorts so they could examine him. The nurses checked the rest of the team out to see if they had received any injuries. They did a complete examination of John and found that he was extremely dehydrated. He also had bruises and welts on his wrists from the restraints that he had pulled on. He had minor cuts on his face and hands. And he seemed to have a low grade fever due to exhaustion. From what Becket had heard from Rodney, Ronan and Teyla he was probably going to have some mental issues as well from what the Ancient device had done to him. It was going to be a long road back. Becket hoped that they could all help him get back to his care free, sarcastic self. Back to the Colonel Sheppard that they all respected and cared for. Because if that didn't happen then their little corner of the Pagasus Galaxy was going to be a lot less interesting to be in.

Becket finished the examination and pulled the blanket up over John's bare chest to keep him warm. Then he attached the IV line on his hand and checked the heart monitor before heading to check on the others to see what the verdict was. Then maybe he would get more answers about what this device was doing to Colonel Sheppard. And was the Colonel truly free of its influence?

* * *

As the night progressed Carson kept a close eye on Colonel Sheppard. The man was not doing very well. The dehydration and the fever were beginning to wreak havoc on his body. What had started off as a low grade fever had slowly been up graded as the night moved on. He could not figure it out. John's symptoms just seemed to get worse. It was beginning to scare him a little. The dehydration did not help matters either. The higher the fever got it seemed to compound the amount of dehydration. He was going through a lot of IV fluid just to counteract what he was losing in body fluid.

At three o'clock in the morning Carson found himself sitting at the pilot's bedside watching the man sleep. Watching him shiver with fever. There was only the night lighting in the infirmary and every time that John moved shadows would bounce around the room.

Carson was caught off guard when he felt a hand rest on his right shoulder. He jumped and turned around to see who it was. He was surprised to see that it was Rodney. The man had seemed to become a very close friend of the Colonel's. Any outsider would think that Rodney and John hated each other. They were constantly throwing insults and sarcasm back and forth at each other and they would yell a lot. But the crew of Atlantis, they knew that Rodney and John respected one another and were very good friends. One doesn't have to act like a friend to be one. Rodney cared for his friends and it was easy to see that he was quite worried about the health of the pilot. In fact, scared was more like it. Scared that he might die.

"Hey there Becket. I was going crazy in my lab so I thought I'd come by and see how

Sheppard was doing." Rodney said as he moved in on the other side of the bed.

"His fever is getting worse Rodney." Came Becket's Scottish lilt which seemed to be getting thicker the more stressed out he was getting.

"How is that?" McKay asked. "I thought it was a low grade fever. Why is it getting worse instead of better?"

"I don't know why. But the combination of the dehydration and the fever is making things a lot worse for him. I've just been sitting here for the last twenty minutes trying to come up with a way to help him. I just don't know."

Rodney reached out a hand and placed it on Sheppard's forehead. He could feel the heat radiating from John. The man was really sick. Carson saw the worried look on Rodney's face and stood up. "I'll let you talk to him alone Rodney. He can probably hear you." Becket turned and left Rodney to watch over John for a while.

Rodney moved around and sat down in the chair that Carson had been sitting in. He just sat and looked at his friend for a while, unsure of what to say to the man. Then after ten minutes of watching John sweat and shiver, he reached a hand out and placed it on the pilot's shoulder. "Hey there buddy, it's me Rodney." He stopped and sighed. "Of course it's Rodney, who else would it be." He sighed again and put his hand through his hair. "Come on man. You have to get better. Atlantis just won't be the same if you're not here. And I need your sarcasm and your hero complex to keep me going. Who else am I going to tease if you're not here?"

John twitched and rolled onto his side, facing Rodney. He saw the bandages on his wrists from the damage done by the restraints they had him in. Then he saw the haggard look on John's face and reached his hand out again and then paused before it reached his face. He brought his hand back and placed it in his lap. He watched the man sleep and then fell asleep himself. His arm on the bed and his head resting on his arm.

* * *

Around four in the morning John's eyes flickered slowly open and he found himself staring into the sleeping head of Rodney McKay. He reached out his shaking hand and placed it on Rodney's head. He smiled faintly and then began to shake uncontrollably.

Rodney woke when he felt something trembling on his head. When he lifted his head John's hand fell limply onto the bed and continued to shake.

"Sheppard? Are you awake?" Rodney asked as he looked at his eyes and saw that they were open. When he saw that John was trembling quite heavily he yelled for Becket.

Carson came running in looking like he had just woken up. When he saw John having what looked like a seizure he ran to the man's side.

"Rodney! Help me out man! We need to stop the seizure."

Rodney jumped up and grabbed hold of John's shoulder. Becket looked into John's open eyes and took hold of his head. "John! John! Look at me. I'm going to help you. Okay?" the doctor said. John's eyes were wide open and there was a slight nod that Becket could see. "Okay then. Let's get going Rodney. Help me stop the seizure."

* * *

It took them ten minutes but they were finally able to stop John from shaking. He lay spent on the bed breathing heavily. The sheets were crumpled around his feet. He was sweating all over and his skin was glistening. His hair was half matted to his face and half standing up on end. He looked like hell. He was staring off into space looking somewhat dazed.

"John, can you hear me son?" Carson asked as he leaned over to check on the Colonel's eyes.

The Colonel slowly blinked and then looked at Becket, then at Rodney. He coughed slightly when he tried to speak. "What happened?" he asked in a raspy, quiet voice.

"You had a seizure Colonel. I'll have to do an examination to find out why."

"You were sleeping when I woke up Rodney. How long have you been here?" John asked as he looked at the man.

"Um…" Rodney did not know what to say. "Just for a couple of hours and I fell asleep."

John looked at him and smiled that crooked grin of his.

"I think we should let him sleep Rodney. Come on." Becket said as he pulled the sheets up to John's chest. Rodney nodded, took one last look at John and left the infirmary. Becket gave John a sedative and then left him to sleep for the rest of the night.

* * *

When John next woke up it was almost eight in the morning. He didn't know that at the time but he looked around at the darkened room. It was empty and quiet. He decided that he needed to use the washroom so he slowly pulled the sheets down and slid his legs over the side of the bed. He sat for a moment, dizziness starting to subside. He pushed himself off of the bed and winced when he felt the pain in his wrists.

When he got to his feet they almost gave out from under him. He held himself steady for a moment by holding onto the IV pole and then began to walk towards the bathroom.

As he stood in the bathroom looking into the mirror he tried to fix his screwed up hair with water and it didn't seem to work the way that he wanted it to. He sighed with frustration and then suddenly grabbed his head. It felt like someone was sticking a hot poker into his brain. He ended up on his knees trying to make the pain go away. It was so intense that it almost knocked him unconscious. Then he began to hear what he thought was a voice inside of his head. He tried to shake it off but it just wasn't working. He felt like he was going crazy.

He tried to stand up by pulling himself up the side of the sink. He fell back onto the floor and grabbed his head again. Then quite suddenly the pain was gone and he was up on his feet in a trance. He left the bathroom and then the infirmary wearing burgundy scrubs. He walked down the hall with Atlantis members staring at him as he went. It was like he had a destination in mind because he didn't say a single thing as he went.

He walked to the Jumper Bay and went directly to Jumper One. When he went inside everything lit up and he sat down at the console. He started up Jumper One and then hit the address for P3J-448.

**TBC in Chapter Eight…**

* * *

**A/N:** Hope you enjoyed the chapter guys. And yes, I am leaving you in a bit of a cliff hanger. Sorry about that. Hmmm, I wonder what could be happening to Sheppard? I guess you'll have to tune in to the next chapter to find out. Ta for now.


	8. Chapter 8

I do not own any of the characters (except for the bad guy of course) any of Stargate Atlantis. Boo hoo. Hey there everybody. It's been an extremely long time since I have done this. So so sorry about that for those of you who were reading this. I think I forgot about it. I put my book away that I was writing this story in and it left my mind because I was writing some all original stuff that has nothing to do with SGA. Then I found my book yesterday and thought that I should finally add on to my chapters. Again, so sorry. But I'm back and hopefully I can finish this story. Yay!

**Chapter Eight**

In the main Control Room the technician and the other members of the crew that were there were surprised when the wormhole engaged. "Unauthorized gate activation!" the technician said over the base intercom system. Weir came out when she heard the alarm going off. "Who initiated the gate?" she asked.

"Someone in the Jumper Bay Ma'am." The technician said.

"Someone here? Without my authorization?" Weir said.

"Yes Ma'am."

"Turn the gate off now!"

"Yes Ma'am." He did as he was told and everyone watched as the gate shut down.

"Get Security to the Jumper Bay now and stop whoever tried to go through the gate."

"Right away Ma'am."

Within five minutes the Security detail was in the Jumper Bay heading towards Jumper One which they could see was lit up and in use. They snuck around the corner with their P90s in position and as soon as they did they were knocked unconscious by a couple of quick blows. Then more Security arrived at the scene and John took off running out of the Jumper Bay.

* * *

In the Control Room the second Security detail came over the com system. "It's Colonel Sheppard Ma'am. Something's wrong with him. He's acting crazy and he's attacking us."

"What? Why was he trying to leave Atlantis?" Weir asked.

"Unknown Ma'am. But he's on foot and probably heading your way to get to the Stargate."

"Understood. Do an Atlantis-wide search just in case. Only the sections that we have deemed safe. And send more security our way to head him off just incase you're right about him coming here."

"Yes Ma'am. We're on it."

She turned to the people in the Control Room and looked around at them. "Okay people. Colonel Sheppard is most likely coming our way. Let's be prepared. And remember, we're only trying to stop him, not hurt him." Everybody nodded. "And call Dr. Beckett, Dr. McKay, Teyla and Ronan in here to help." They nodded again and headed off to work on their tasks.

* * *

When Rodney, Teyla and Ronan arrived they knew that John was being taken over by Puren again. "The big fat liar." Rodney said as he leaned against one of the consoles.

"We knew there was a risk McKay." Ronan said with a frown.

"I know. But just once I'd like a bad guy to tell the truth. And I know that's wishful thinking on my part. Now we've brought an evil Ancient Device back to Atlantis and we don't know how to get rid of it except go to the planet and blow it up. And that would most likely kill Sheppard. What do we do?"

"First we subdue Sheppard." Ronan said. "Then we worry how to get Puren out of him."

"You're not going to hurt him are you?" Rodney asked. Ronan looked at him as if he had asked a really stupid question. Rodney shrugged. "I'm just asking."

"No. I'll subdue him without hurting him significantly. I can't say he won't get a bruise or two but he will be relatively unharmed. What do you take me for McKay?"

"Do you really want me to answer that?" McKay said with some sarcasm. Ronan stared at him with a frown and an upraised right eyebrow.

"Alright! Enough guys." Weir said. "This doesn't help matters does it? I mean really." Rodney sat down hard and closed his mouth before he would say anything else that would be construed as stupid to anybody else. "Alright. Now John is heading this way. So let's just be prepared for him so that we can get him back to the infirmary."

"I suggest that we place guards on the Stargate as well as in here Dr. Weir." Teyla said matter of factly.

"I agree Teyla." Elizabeth said as she crossed her arms. "So Ronan, why don't you go with two of the Security detail and watch the gate. Take who you think will be the best help to you in capturing Colonel Sheppard." Ronan nodded grimly and moved off to find the two people he would use. "Teyla. You stay here with Rodney and make sure he doesn't get to the controls." Teyla and Rodney nodded their consent to her plans. "I'll coordinate on the coms. And let's hope that he hasn't snagged any. Or he'll hear all of our conversations."

They shut down all non-essential parts of Atlantis as well as the main gate system. When they were finished, only secondary lighting was on and the DHD was put under password control. With only Weir knowing what the code was. It felt strange to them to have to be on alert from their Military Commander. All of Atlantis was on edge and scared that something would happen to Sheppard. That he would be killed by whatever was controlling him.

* * *

Ten minutes had gone by since they had been notified that John was headed in their direction. John would be there any minute and they knew it. And just as Elizabeth thought that same thought a crash came from behind them. Elizabeth and Rodney turned from the balcony overlooking the Gate Room and saw John standing in front of them, a security guard unconscious on the floor in front of him and a P90 in his hands. They backed away from him slowly and Weir turned her head slightly to look down at Ronan. She gave him a tiny nod and she saw him nod back. They could see how disheveled John looked. He was still wearing the burgundy scrubs from the infirmary and he had no shoes on. He was in bare feet. A majority of his dark, spiky hair was standing up on end from sweat and the scrubs looked wet in areas too. He still had a fever but he was acting like he didn't know. His eyes looked wild. Completely unlike what they normally looked like. They could see that Puren was in complete control of the Military Commander of Atlantis.

"John. Just stay calm." Weir said with both of her hands up in the air.

A lopsided smirk formed on the man's face. "Now, now Dr. Elizabeth Weir. You know who I am and who I am not."

"Yes I do. And I want to know why you insist on staying inside Colonel Sheppard?" she said as she put her hands down at her sides.

"Because he is my power source. He will keep me alive. I thought you all knew that by now. Especially you Dr. Rodney McKay. Or was I wrong to understand how smart you were?"

Rodney just stared at him with hate. "No, I am smart and I know that you are a lying bastard."

"Oh that hurts Rodney McKay."

Rodney shook his head. "Are you really that intent on being blown up? Cause I told you what would happen if you did anything to harm Sheppard. I told you what would happen if you didn't leave him alone."

"Yes you did. And I thank you for that. Really. But I don't believe you because if I die he dies. And you know that."

"Do I?" Rodney said.

"Yes you do. And that's why you haven't done anything to me yet. You are afraid that he will die. And I know you do not want that. You are all close to him."

Teyla, Rodney, Weir and the rest of the people in the Control Room just stared at Sheppard with a mixture of hate and worry. They hated the thing that had taken him over but they were worried for their friend.

"I think it's about time you dialed the address for my planet. I must get back to my body."

"Oh. So now you have a body?" Rodney said as he moved a little closer.

"My structure is my body. Yes. I thought that you were the type of person who thought outside the box Rodney McKay?" Rodney did not answer that question.

"We are not going to let you take John back to your planet Puren." Dr. Weir said as she moved up beside Rodney.

"Oh but I think you will Elizabeth Weir."

"Don't be so sure Puren." She said as she saw Ronan and the two security guards deftly move in behind Sheppard. She kept her eyes focused on Sheppard so as not to give them away. Ronan pointed his fingers at one guard and then pointed to the left. The guard moved that way. Ronan then pointed his fingers at the other guard and then to the right. The guard went that way. Ronan moved up the centre by himself. They came closer to the Colonel and before he could react Ronan jumped him. The two guards circled around in front, grabbed the P90 out of his hand and aimed their own weapons at him.

John began to yell out and struggle in Ronan's grasp. Ronan pushed him down on the ground and forcefully pulled his arms behind him. He pushed his knee into John's back and held his hands against his back as well. "Ahh! Let go of me now! Let go!" he yelled out.

"I don't think so Puren." Ronan said. "You aren't going back to the planet. You won't take Sheppard back there. You should know by now that we will find a way to extract you from him. We will destroy you and Sheppard will live."

"Ahhhhh!!" Sheppard yelled out.

"Take him to the infirmary." Weir said. "And get Beckett to restrain him so he can't get back to the planet. That's all we need is for him to get back to his body."

As they wheeled John down the hallway restrained to a gurney he was bucking constantly, trying to get free. Ronan was keeping a hand on him the whole way to make sure that he didn't get free. Teyla, Rodney and Weir were following close behind them. They could see fresh blood forming on the bandages on his wrists. He was pulling extremely hard.

"Calm down! Just calm down!" Rodney yelled out.

By the time they had made it to the infirmary his wrists were totally bloody. They quickly undid the restraints and moved him to a bed. Then they did up the restraints again on his

wrists and on his ankles. They could not get him to calm down. He was going completely crazy.

"I think we need a sedative right away." Beckett said to a nurse. She took off running and came back with a syringe full of clear liquid. She gave it to Beckett and he asked Ronan to hold John down so that he could administer the sedative. Ronan leaned over the pilot's chest and held him down, then grabbed hold of his left arm so Beckett could move in. The whole time the sedative was being injected John was yelling out.

When Beckett was finished Ronan stood back up and looked at the man lying in front of them. Becket looked at Ronan and saw a look that he had not seen before on the Runner. Fear. If this situation could instill fear in Ronan Dex then they had a huge problem.

**TBC in Chapter Nine…**

* * *

**A/N:** This isn't really a cliff hanger but I thought it was a good place to end. Ooooh. Things are getting interesting. Puren really wasn't bye bye. The big liar. But I'm sure you probably already figured that one out. How do you think they're going to get rid of him? It's still kind of a mystery to me. So you'll have to wait and see. Ta for now guys. And don't worry, I have another chapter already to go. :)


	9. Chapter 9

I do not own SGA or any of it's characters. The only thing that I own would be my bad guy. I said it didn't I? I had another chapter ready to upload. Okay so this is a short chapter. I'm tired. What can I say. I didn't want to type anymore. But I will probably be adding some more tomorrow. Hopefully you folks will be reading this again because I was liking your input. So ta for now. Hope you enjoy. :)

**Chapter Nine**

After ten minutes of yelling and freaking out John slowly began to calm down. The yelling began to dissipate and his eyes fluttered. Then finally he passed out. He became dead weight.

"Good. Now maybe we can fix those wrists up." The Scottish doctor said. "And see what else is going on in his body. We need to examine him right away." Ronan grunted and moved away. Then Weir, McKay and Teyla followed him out of the infirmary.

* * *

An hour later the four sat silently in the conference room. Ronan was leaning up against the wall with his arms crossed in front of him. He was staring at the floor with a frown on his face. Rodney sat in one of the chairs with is arms crossed on the table and his head on his arms. Teyla was sitting in her chair with her arms resting on the chair at her sides. She was staring at the table. Elizabeth was sitting a lot like Rodney was except that her chin was resting on her arms. They had been unable to think of anything to say to each other after the first ten minutes. They had been too worried for John and had no idea of what plan to come up with to help him. Ronan had been right when he had said that if Puren died John would too. So they had to think of a way to extract Puren before killing him. They were out of ideas. In fact they never had any to begin with. They just looked extremely bored while they were waiting to hear about Sheppard.

Rodney sighed and then turned his head to face Weir. "Beckett better get here soon because I want to know how Sheppard is doing."

"Me too." Elizabeth said.

Just then Beckett came through the entrance to the conference room as if he had heard them. The three who were sitting immediately stood up and Ronan moved away from the wall and stood with his arms crossed, waiting for the news.

"Oh. Well. I'm glad you're all here." Beckett said. "I've got good and bad news for you all. What do you want to hear first?"

"Let's just hear the good news first Carson." Weir said.

"Right." He said. They just stood and looked at him. "Well. The good news is that Colonel Sheppard is not any worse off than he was before. His fever has not upgraded. And that could be a good sign."

"And just what is the bad news Carson?" Rodney asked with a mix of curiousness and fright in his voice.

"He doesn't seem to be getting any better. And I'm afraid that if this Puren character gets the Colonel back to it's body that will be the end for the Colonel."

"Wow." Rodney said. "When you say there's bad news you really go all out." He sat down heavily in the chair that was behind him. Beckett creased his brow and let the impact of his information settle in.

"There has to be a way to get this thing out of Sheppard." Ronan spoke up. "We can't just let it kill him."

The four looked at the Satedan with surprise at the outburst. They really did not know how Ronan felt about John. Now it was evident that he liked the pilot. Did not want anything to happen to him. That was encouraging. And it was so like Sheppard to have this kind of an effect on people. Most people gravitated to him like a moth to a flame. He was charismatic that way. Ronan was charismatic in his own way too. He may seem like a big brute at first meeting but he was highly intelligent, a fierce fighter and a devoted friend when he chose to be somebody's friend. He had chosen the people of Atlantis as his friends. As his teammates. And he had respect for Sheppard and the rest of SGA-1 as well as Elizabeth. He was a great ally to have. And they all knew it, even Rodney who always seemed to get on the wrong side of the Satedan. Ronan looked at their surprise and raised his right eyebrow. He did not seem embarrassed by the revelation.

"I agree with you whole heartedly Ronan." Weir said finally. "I'm sure we all feel the same way. Our only hurtle at the moment is how do we get rid of Puren without killing John."

"We live on Atlantis Elizabeth." Rodney said matter of factly. "There has to be something we can use here to get rid of an Ancient Device, without blowing it up or smashing it to itty bitty pieces."

Elizabeth thought about what he had said for a moment and then a light seemed to come on in her mind because her eyes lit up. "I want everybody to do a search of Atlantis. Every nook and cranny that they can and see if we can find anything to use. And hopefully it will be something that Puren can't figure out. Split into groups of two or three. I want at least one scientist and one of the Military Detail on each team. Ronan. I want you, Teyla and Rodney to stick together. See what you can find. And I want the three of you to be in charge of the teams. Understood?" The three nodded at her and hurried off to begin the plan. To set it in motion. "Carson. I want you to stay with John. Keep a close eye on him and Puren. If he wakes up again I want you to sedate him. We don't want him figuring out what we're up to."

"Aye." Beckett said as he turned to leave. Then he turned back and looked at her. "I hope this works Elizabeth, because if it doesn't we will have no other choice but to get rid of Puren any way we can. Then at least Colonel Sheppard will be at peace."

"Let's hope it doesn't come to that Carson. Because Atlantis without John Sheppard would be nothing. We all know that he is the heart and soul of this expedition." He smiled at her remarks and placed his hand gently on her shoulder. "Aye dearie. I know exactly what you mean." She put her own hand up to the one on her shoulder and grasped it. She smiled and then he was off to stay with John.

She slumped down in one of the chairs and put her elbows on the table. Then she raised her arms and put her face in her hands. She began to cry. She knew in her heart that she could not lose John Sheppard. Knew deep down in her heart that there was love there. She would be devastated if he were to die. Absolutely devastated.

**TBC in Chapter Ten…**

* * *

**A/N:** So sorry for the short chapter. But it is late and I'm tired. It's beddy bye time. Time to dream. But tomorrow is a new day and I should be typing again. Plus tomorrowis a holiday, so even better. And this seemed as good a place as any to end the chapter. So good night. Hope you enjoyed. Later days. :)


	10. Chapter 10

I do not own Stargate Atlantis or any of its characters. The only thing that I own is the bad guy, a few of the made up people and my story. Hey there folks. It's me again. I've reached a point where I have nothing left that is written down. So I will be posting three chapters. Then I'm going to have to start writing again so that I can finish this. Here's hoping that I don't get writers block. Because that would suck. I hope you like where this is going. Have fun reading everybody. :)

**Chapter Ten**

Almost two hours later the remainder of SGA-1 had pulled the entire contingent of Atlantis together, minus the techs keeping an eye on the Control Room and the Stargate and the infirmary staff who was keeping an eye on Sheppard. They had been separated into teams of two or three as per Weir's instructions and had been sent off one group at a time to various sections of the floating city.

SGA-1 were about halfway through their job when Weir arrived to check on their progress. "How are things going Rodney?" she asked as she moved in beside him and crossed her arms in front of her.

"Things are going great Elizabeth. Half of the city is already out there searching."

"Wow. You guys move quickly." She said, impressed.

"We have told people to report to us here at certain times so that we could put them in teams and send them off." Rodney reported.

"Everyone is eager to do this when we tell them what they are doing this for." Teyla said. "They want to help Colonel Sheppard any way they can."

Rodney spoke up again as he moved over to the main screen in the room. "We give each Military delegate a P90 and a service pistol. And each scientist is told to stay with their team. And they are to bring anything they deem necessary for the search."

"Where are the three of you going to head after you're done here?" Weir asked.

"We're going to go into one of the lower sections of Atlantis. One that we've been trying to get to for a while now. You never know, it could hold something that could help the Colonel."

"Lets hope so." Weir said. "Well, I'll leave you to finish here. Don't forget to check in with me every fifteen or twenty minutes on your progress."

"We won't. And we've told everyone else to do the same too. We don't want anybody getting lost." Rodney said.

Weir nodded and then left them to set up the next team which had arrived. It was going to be a long day but well worth it as far as she was concerned.

* * *

Over in the infirmary, Dr. Beckett was putting a cold compress on John's forehead and was trying to get his fever to go down. The pilot had been sleeping since he had been given the sedative but had been shifting around a lot either from Puren, the fever or both. His wrists had been bandaged up again after he had been put to sleep. The restraints, however, had been put back on. His ankles as well had been bandaged up but they were not as bad as his wrists.

Beckett watched as the Colonel twitched from dreaming. Puren was most likely moving around in his mind trying to get more information and John was trying to stave him off. He sat for a moment and watched the pilot sleep.

"Do you need me for anything else Dr. Beckett?" one of the nurses asked as she came up behind him.

He turned to look at her. "No. That's okay Jennifer. Melissa should be here soon to cover your shift. You go on ahead and see if you can help at all with the search. I'll be okay. Don't worry."

She nodded her head, smiled and then left the infirmary to help find a way to get the creature out of Colonel Sheppard. Carson reached out again and placed a fresh cold cloth on John's forehead.

* * *

Not long after Jennifer left the infirmary, Beckett caught movement out of the corner of his eye. He turned to face the object of the movement and saw that Sheppard was fully awake. Beckett started when he saw the look on his face. There was a look of pure hate on his face. A look that was not normal for Sheppard.

"So you are the doctor that has been looking after this body. Hmm. I do not think that you are doing a very good job. This body still sickens."

"Gee. I wonder why that would be." Beckett said in a very thick Scottish accent.

"You are being sarcastic. I do get that. I am learning quite a lot from Colonel Sheppard. But there are still things that he is keeping from me. Things that he is putting a wall around. I will get to them eventually." Beckett just stood where he was and watched the man. "You know I will get out of these restraints. It is inevitable."

"I don't think so Puren. You are going to stay there until we can think of a way to separate the two of you."

"Let me out now and I will let Colonel Sheppard live."

"No. Rodney told me you said something like that before. And you obviously didn't tell the truth."

"It was necessary to keep my hold on Colonel Sheppard. I was not yet completely awake. Dr. Rodney McKay thought that he had made an agreement with me but he did not."

"I'm still not letting you go. Forget it."

"You will let me out NOW!" Puren yelled out and yanked as hard as he could on the restraints. If Colonel Sheppard were awake that would have hurt tremendously.

Beckett jumped back at the outburst. He put his finger up to the com in his ear. "Dr. Weir. I'm in need of assistance. Colonel Sheppard is awake. Or rather Puren is awake. Can you send a couple of the security detail here to help me out?"

"Right away Carson." Came Weir's voice over the com system.

Sheppard began to buck on the bed and by the time the detail had arrived, Beckett was holding him down unsuccessfully. The two men raced over to the bed and grabbed hold of Sheppard's arms.

"Hold him down tightly for me gents. I need to administer another sedative. Just be careful and don't hurt him. Or at least try not to."

The whole time John was bucking in the bed. It made things extremely difficult for the doctor. When he was finally able to give John the sedative the two men let go of him. This time it didn't take long for the sedative to take effect. Within minutes John's eyes began to close and then he was out cold.

Beckett sighed and looked at the two men on the other side of the bed. "Thanks gents. He really is tough when he wants to be." They nodded at Beckett and then began to leave. The doctor stopped them. "Hold up. Can you just wait outside the infirmary? If he wakes up again I'm going to need your help."

"No problem Doc." One of them said. The two of them made their way outside the entrance and stood there, waiting.

Inside, Carson pulled the sheets back up to Sheppard's chest. Then he checked his wrists and ankles again. No bad damage but there was a little bit of blood showing through the wrist bandages. If he kept pulling on those restraints he could do a lot more damage. He sat and thought for a moment. He knew that he had to keep him sedated. There would be a lot less damage to John if he stayed asleep. He made his way back over to his office just as Melissa, the nurse, showed up.

"Is everything okay Dr. Beckett? I saw the security outside."

"Aye. Sheppard just woke up again is all. I needed them to help me sedate him."

"Is he asleep now?"

"Aye. He is Melissa. I'll be in my office. Will you please keep an eye on him?"

"Of course."

He nodded and headed off to his office for some coffee.

* * *

Down in the lower depths of Atlantis Teyla, Ronan and Rodney were searching a new lab that they had found. They had been there for fifteen minutes after they had left two previous labs which they got nowhere with.

"We're not going to find anything here." Rodney said as he placed another device down on the table he was standing in front of.

"Don't be so negative McKay." Ronan said as he looked up at the physicist. Completely annoyed at this point.

"I'm not being negative. I'm telling the truth. This place is a bust."

"Rodney, we have only been looking for fifteen minutes." Teyla said. "How can you be sure we have looked everywhere?"

Rodney sighed and looked back at his teammates. "Fine. Let's look for another half-an hour and see what we come up with." He turned back to the table and picked up another device. He was getting extremely frustrated.

* * *

Half-an-hour later they still had not found anything that they could even remotely use. The lab was a bust and they all knew it.

"Well. I believe we have one more room to check. So let's go." Rodney said as he moved towards the entrance.

"Wait McKay. I see a back entrance over here. This could either be a closet or another room." Ronan said from across the room.

Rodney turned at what the Satedan had said and then hurried over to his side. Teyla followed. When all three of them were standing in front of the door, Ronan reached out his hand and placed it on the pad to the left of the entrance. It glowed and the door opened. When they entered they saw what could have been another lab. The lights came on as they slowly moved through the room. They stopped in their tracks when they saw pods around the perimeter. They were the size of a human being. They moved to the centre of the room and stood looking at the pods. A main control panel stood to the right of them. Rodney walked over to it and placed his hand on it. When it lit up, so did the pods.

"Okay. What is this place?" Rodney asked.

Ronan and Teyla moved off to look at the pods. Teyla placed her hand on one and it felt cold. "I do not know." Teyla said answering Rodney's question.

"Could this be what we're looking for?" Ronan asked as he continued to look at the pods.

Rodney looked at him and then back at the console. His eyes lit up. "I know what this is!" he said excitedly as he snapped his fingers together in quick succession. "I know exactly what this is!"

Both Teyla and Ronan looked over at him and then rushed over to where he was standing. "Was Ronan right?" Teyla asked. "Will this help Colonel Sheppard?"

"It will! It will!" Rodney yelled out. "We have to get back to Weir now and tell her what

we've found."

"What have we found McKay?" Ronan asked with exasperation.

"I'll tell you once we're all together. Us, Weir and Carson." He said and rushed out the door. "Just remember where this lab is so we can get back here easily."

Ronan and Teyla took off running after Rodney trying to get answers out of him as they went.

**TBC in Chapter Eleven…**

* * *

**A/N:** Well I guess you're going to have to wait until the next chapter to find out what the device does. Sorry to leave you hanging, but that's just the way things go. But don't worry, I'm going to be posting more. You'll never guess where this is going. The wheels are turning in my brain as we speak on what I'm going to do with this story. So ta for now folks. Later days. :)


	11. Chapter 11

I don't Stargate Atlantis or any of it's characters. I only own my badguy and my story. Well, what did I tell ya'll. I'm posting again. Didn't have to wait to long to see what I've come up with. Hope you like cause I totally know where I want to take this. It's going to be awesome:)

**Chapter Eleven**

Half-an-hour later the team were seated around the table in the conference room along with Dr. Weir and Dr. Beckett. They were all waiting for an answer from Rodney. They were getting quite impatient.

"Will you just tell us already Rodney!" Weir said.

Rodney sighed and began to speak really fast. "Okay. So those pods down there are mind transfer devices. And you're asking me how I know this. It's quite easy really. I read what the console had to say even though it was all in Ancient and I was able to translate everything that it said. And I was able to download the information over the data net and get it onto my data pad. We just have to put Sheppard in one of the pods and start it up. Then we should be able to extract Puren out of his mind." The others just sat and watched him as he babbled on.

"Is that all Rodney?" Weir asked. "Because I don't think you took a breath during that whole explanation."

He was breathing quite heavily with excitement. "Sorry. It's just that this is really the way to save Sheppard. I know this will work."

"Okay. But we have to go through every bit of information with a fine tooth comb. There has to be no way that this can backfire on us. If we find out anything that hinders this plan we will not move forward with it. Got it?"

"We've got it Elizabeth. Don't worry." Rodney said as he sat up straighter in his chair and could hardly keep his excitement inside.

"Okay. Then let's get started before Puren makes us do something that we regret." Elizabeth said and they all stood up to leave the conference room. "And everybody be careful. I don't want anybody to get hurt while we are working on this." She said before they left the room.

* * *

Rodney turned and saluted her. Telling her that he understood. Then they all left the room.

The team ran check after check after check on the device trying to deem it usable. It was a very slow process and to SGA-1 it was the slowest process that they ever had to wait through. They wanted to be able to help Sheppard now. Not wait forever until they got the go ahead. Rodney ran numerous tests with the help of Teyla and Ronan and they were getting quite exhausted with the whole situation.

"Dammit! Why isn't this working?" Rodney said with exasperation. "Why in hell isn't this working?"

"I don not know Dr. McKay." Teyla said. "Maybe we are missing something."

"Of course we're missing something. But what are we missing?"

The three members of SGA-1 stood in front of the main console in the lab and stared at it. They had no more ideas left. Even Rodney was at a complete stand still.

"Let us go see Colonel Sheppard then Dr. McKay." Teyla said. "Then maybe we will come up with something."

"Yes. I agree with Teyla on this McKay." Ronan said as he walked away from the console towards the door. He stood there with his arms crossed waiting for the other two to join him. Teyla walked over to stand with him and the two of them stared at Rodney. McKay finally nodded his head, put his equipment down on top of the console and followed his teammates out of the door and into the hallway.

"Let's hope that he looks better than the last time that we saw him." McKay said as he turned to face them.

"We can only hope Dr. McKay." Teyla said as she put her hand on his shoulder and turned him around, pushing him towards the transporter to the upper levels.

* * *

When they reached the infirmary they slowly made their way in and spotted Dr. Beckett in his office. "Hey there Carson." Rodney said. "How's our Colonel doing?"

Beckett looked up with a smile when he saw the three friends walk in. "Rodney. Nice to see you three. But what are you doing here? I thought that you were working in the lab."

"We were Dr. Beckett." Teyla said. "But we have run out of ideas. We thought that coming here to see John would give us some."

"He's sleeping still. We have to keep him under sedation so that Puren won't wreak any havoc and so that we won't hurt Colonel Sheppard."

"That's fine Carson. Really." McKay said. "We think that just being around him will help us come up with an idea or two."

"Alright then. Go on and sit with him. I'm sure somewhere in the back of the Colonel's mind he is there listening to us."

All three of them nodded in unison and left the office. When they made it to John's bed they saw that he was still strapped to the bed by the restraints. Ankles and wrists were covered in bandages because of the constant rubbing and pulling by the patient. His hair was still disheveled and part of it was matted to his forehead. The sheets were up to his chest and they could just see the wires attached to his chest to record his vitals. He also had a tube in his nose to help him breathe. He wasn't sweating as much but he still looked pretty sick.

Teyla walked up to him and placed her hand on his forehead. She kept it there for a moment and could feel the heat. She knew that he had been sick before they had gone to Puren's planet. But Puren had made things considerably worse for him. Ronan stood with his arms crossed in front of him and stared down at Sheppard. You could not tell how he was feeling. His face was almost vacant. Rodney stood beside the bed for a moment and then decided to sit instead. Nobody said a single word for almost five minutes. They were all unsure how to progress.

They continued to watch John sleep and they saw his chest rise and fall. The team hated to see their CO look like this. So pale, so sick.

Rodney finally spoke up. "So. Has anyone come up with an idea yet?"

Broken out of their reverie the two looked at the physicist. They shook their heads in unison.

"Yeah. Me neither." He said shaking his head. Rodney stood up suddenly and began to pace. The others knew that when Rodney paced he was trying to come up with an idea. Then he began to babble. An even bigger sign that an idea was trying to form in that brain of his.

Teyla and Ronan just sat staring at the man trying to piece together what he was trying to say. It seemed extremely random to them. But then again, it was Rodney. It made sense in his head. It didn't necessarily have to make sense to them. It was Rodney's way of thinking.

They looked at each other and then back at him. "Rodney. I think it is time to go back to the lab." Teyla said as she stood up. Rodney did not seem to hear. He began to babble even more.

"McKay!" Ronan said loudly and sternly so that the man would hear him. Rodney suddenly stopped talking and pacing and looked at his friends.

"It is time to go back to the lab Dr. McKay." Teyla said as Ronan stood up beside her.

"Right. Right." McKay said quickly. "Let's go." And just as they were about to go a hand reached out and grabbed hold of Rodney's wrist.

**TBC in Chapter Twelve….**

* * *

**A/N:** He he he he! Who could have grabbed Rodney? Do ya'll know? I bet you can guess. TTFN. Later days. :)


	12. Chapter 12

I don't own Stargate Atlantis or any of it's characters. I do, however, own my badguy and my story. So here's the last chapter that I have written at the moment. I will try to write more so that I can post soon. As I said previously I have ideas purcolating in my brain. So hopefully I'll have something soon. Ta. :)

**Chapter Twelve**

"Having a hard time coming up with an idea Dr. Rodney McKay?" came a familiar voice from beside them.

They all stopped in their tracks and Rodney tried to pry his wrist from his friend's strong grip. John pulled him towards the bed and the man lost his footing and went down hard to the floor. Ronan tried to grab him before he fell but was unable to move fast enough. John let go before the man landed and there was a large lop-sided grin on his face.

"Dr. Beckett!" Teyla yelled out. "We need you now!"

Ronan and Teyla each took hold of one of Sheppard's arms and held on tight even though he was strapped down. Rodney was slowly trying to get up off of the floor. "Ow! Man in pain here. Man down!"

Beckett came running in to the room with a nurse in tow and saw the commotion. "What happened?" he asked as he came up beside Ronan. The nurse ran to Rodney's side to try and help him to his feet.

"Puren woke up." Teyla said. "He grabbed hold of Rodney as we were trying to leave and pulled him down."

"Quick Susan. Grab another sedative." Carson said to the nurse. Susan left Rodney's side and ran to the shelf to get a needle.

John was yelling. Or rather Puren was. "YOU WILL NOT HAVE THIS BODY! YOU WILL NOT TAKE HIM FROM ME!" He began to struggle so much that the veins in his neck were showing and his wrists were severely bleeding. They looked down at his ankles and saw that they were bleeding as well. The restraints were cutting him. Then quite suddenly one of the wrist restraints broke and Ronan lurched as the arm came free. His hand clamped onto Ronan's neck with surprising force and strength. Ronan tried to pull the man's hand off and was completely surprised when he could not. Apparently Puren gave John Sheppard amazing strength. Much more than he previously had. Ronan tried to speak and found himself unable to.

Teyla tried to help him but to no avail. Ronan's vision began to blur and he looked down at his friend. He saw the evil in his eyes. Evil that he had never seen in those eyes before. The fingers squeezed tighter and Ronan's vision went hazy. The Runner could barely hear the commotion around him. Things seemed to be in slow motion. Then before anyone knew what was happening, Ronan was going down. John let go and Ronan crumpled like a stone.

The two security detail at the door had rushed in while all of this was happening and were trying, along with Teyla, to free Ronan. When Ronan had landed on the floor they tried to get a hold of their CO. The two security guards were hurled in different directions and slammed into the walls for their effort. They did not get back up. Teyla got a surprise backhand across the face and she too flew backwards with enough force to hit a table of equipment behind her. She lay on the ground with her eyes squeezed shut in pain.

While Puren was distracted with the other people in the room, Carson grabbed the needle with the sedative in it and drove it into John's arm before Puren could react. Within minutes John was out cold again.

* * *

In the aftermath, Carson and his nurse were the only ones standing. A slow moving Rodney raced to Teyla's side while Carson went to Ronan and his nurse went to the two security guards.

Ronan lay on the floor on his left side and Carson knelt down beside him. He checked for a pulse and was relieved to find one. If he hadn't have found a pulse everyone would have been devastated. Especially John who would have been technically responsible for a friend's death. Carson moved Ronan onto his back and saw the large bruise in the shape of a hand forming around his neck. The man had lost consciousness due to a lack of oxygen. Who knew that Sheppard was capable of that much force.

Then there was Rodney, who looked like he was in some pain from his incident with John. Carson watched as the physicist leaned over the prone form of Teyla. He was panting heavily. Rodney reached out a hand and placed it on the Athosian woman's shoulder. "Are you okay Teyla?" he asked with concern. He saw a rather large bruise beginning to form across her left cheek.

She grimaced, moaned and then slowly opened her eyes. "Yes Dr. McKay. I believe that I am relatively unharmed." She said in a haggard voice.

"It sure doesn't look like it. You have one nasty bruise on your face. And you hit that table with a lot of force. How is your back?"

"It is sore, but I believe that I will be okay. Can you help me up please Dr. McKay?" she asked as she reached her hand out.

He took hold of her hand and then slowly helped her to her feet. She was unsteady for a moment and then she seemed to collect herself. They helped each other over to where Carson was now trying to fix the restraint that had broken when Puren had attacked them. "How are Ronan and the Colonel?" Rodney asked.

"I have not had a chance to fully look over either of them yet Rodney. How are the two of you?"

"We'll live Carson. Well, Teyla will at least. I think Puren did something to my wrist. It hurts like hell. And then there's my back. Don't get me started about my back."

"Rodney. You didn't fall on your back." Carson said with a look of exasperation.

"No. But I still hurt it." Teyla rolled her eyes. Rodney did not see the quick movement.

"Well you'll have to wait I'm afraid. First we have to look at Ronan and Colonel Sheppard. Then there are the two security guards over there."

"Well then let's get going before something else happens." Rodney said hurriedly.

Beckett's thoughts were running on over time. Puren had to be purged from the Colonel soon or more members of the SGA were going to be harmed or even killed by him. Things were getting out of control. And he couldn't keep sedating Sheppard or there would end up being some permanent damage.

Carson, Teyla, Susan the nurse and Rodney all managed to get Ronan off the floor and onto one of the infirmary beds. Carson then began to check him over to see what kind of damage John had caused. There was, of course, the bruises. On further inspection he found that his larynx was slightly crushed as well. But he would eventually heal. Ronan would not be able to speak normally for a while. He would most likely have to whisper when he spoke. When Carson told Teyla and Rodney they were naturally upset but not surprised. "It's not like Ronan is a chatterbox Carson. I don't think he'll have too much of a problem with it. But just how the hell did Sheppard, sorry… Puren. Just how the hell did he break free? And where did all of that strength come from? It's not like Sheppard is this massively strong guy. I mean, usually it's Ronan doing the ass kicking. Not the other way around. And now a second member of our team is down and out for the count. And might I add, our strongest member."

"I don't know what to tell you Rodney." Beckett said. "Puren must be affecting the Colonel on many different levels. That is the only way that I would say he was able to get the drop on Ronan. And that added strength is why he was able to break the restraint. Susan is trying to tend to Sheppard's wounds. I don't like the fact that everytime Puren wakes up the Colonel loses more blood. And this time the cuts were really bad. This just makes things worse for the Colonel. Much worse. And it doesn't help Ronan either."

"Great! That's just great!" Rodney said as he placed his hand on his lower back.

"Do you want me to take a look at that Rodney? Or can ye wait until I've looked at the others?" he asked the physicist with some sarcasm in his voice.

Rodney just looked at him with his eyebrows raised. Beckett took that as a sign and he sighed. He walked over to the man and led him over to one of the beds to their left. By the time he was done with the examination on McKay the nurse, Susan, had come over to tell them the news about Sheppard.

"I was finally able to stop the bleeding on both his wrists and his ankles. But I don't think he can lose much more blood. The cuts are pretty deep, especially on the wrist that broke free. They're bandaged up again but I don't think the restraints will help much."

"Thank you Susan. You can go on your break now." Carson said as he took the notes on John from her hands.

"Call me if you need me Dr. Beckett." She said and turned to leave them. Beckett smiled as she left and then turned back to the remaining members of SGA-1.

"I think it's best you two head back to the lab. The quicker we get Puren out of the Colonel the better. I'll keep an eye on Ronan and the Colonel. And I'll let Dr. Weir know what has happened."

Teyla and Rodney both turned to look at Ronan and then John They nodded their heads in silence and then left the doctor to tend to their teammates. They knew that Puren was getting stronger which meant that there was a time crunch. They had to get that machine working one way or another.

When they reached the entrance to the infirmary they turned back one last time to look at Ronan and John. They glanced worriedly and then turned back, heading out the door and down the hall.

Carson watched them leave with a mixture of sadness and worry. He could see how truly frightened the two were for their friends and teammates. He only hoped that they could figure out the machine before it was too late. He smiled wanly and then headed over to check on John and his new injuries.

* * *

Not long after Rodney and Teyla had left the infirmary, Dr. Beckett walked into Dr. Weir's office and sat down in the chair across the desk from her. He had a grave look on his face as he stared at Elizabeth.

She had been waiting for the man to show up. Had been waiting for the news that he had for her regarding Ronan and Sheppard. "Well. What's the verdict Carson?" she asked with concern.

"Ronan has still not woken up. But he should soon enough. He won't be talking in his usual manor though. He'll have to give his larynx time to heal. Puren used a lot of force when he was holding onto his neck. He'll have some good sized bruises for awhile on his neck too. And I don't know how he'll feel with the fact that John bested him. I don't think he'll be embarrassed, he'll just be ill-tempered for awhile." Elizabeth smiled at the comment. "What's so funny?" he asked.

"Ronan's not Mr. Cheerful Carson. When was the last time you saw him crack a smile?"

He thought about it for a moment. "Exactly." She said. Carson smiled back and shrugged. "How is John?" she asked changing the subject.

"Ah. That's a different story lass. Let's just put it this way, we won't have our Colonel much longer if we don't get Puren out of him. Puren has healed the Colonel's previous illness but the man is growing weaker by the hour. And I mean the Colonel. Puren is getting stronger and Colonel Sheppard is getting weaker. I don't know how much longer he can last. And it doesn't help that every time Puren wakes up the more blood the Colonel loses from the restraints. I don't know why he won't heal the wounds. It's just not good. Not good at all."

"Um… Carson. I get everything you're telling me, but what previous illness are you talking about?"

Carson sighed. "I guess ye did'na know, but he had a slight flu. I didn't know until after he came back from the planet. What else is new there. When I did the workup on him I saw it. All the signs were there. And I think that's what made it easier for Puren to invade him. He was already in a slightly weakened state."

"That's great. He doesn't tell anyone he's feeling sick and ends up unknowingly letting himself get taken over by an evil Ancient device. I really wish he would start telling us these things. Then he wouldn't get in to as much trouble." She sighed and sat back in her chair.

"That's Colonel Sheppard for you. Not wanting to let anyone in on the fact that something's wrong. Just so that he can be there for his team and the rest of Atlantis."

"What about the others. How did they fare against Puren?" she asked.

"Rodney has a sprained left wrist and he pulled a muscle in his lower back when he fell. He'll be okay though. Teyla has a good sized welt across her left cheek where the Colonel hit her. She also has a nasty bruise on her back from where she hit a table. But she should be okay too. At least she says she can continue her work. She doesn't have a concussion. There wasn't enough force. Preston and Mills, the two security guards, are still unconscious. They hit the walls rather hard. They both have concussions. Plus Preston broke one of his ribs and Mills broke his right arm. They won't be of anymore help to you for the time being."

"Well thank you for the update Carson." She said and then sighed. "You know, when we get John back he's not going to be a very happy camper. He's hurt people and he's not even aware of it."

"That's not entirely true Elizabeth."

"What do you mean?" she asked sitting forward and placing her elbows on the desk, her chin in her hands.

"I think that Colonel Sheppard is aware of everything that is happening to him. And what he is doing to others."

"How do you know that?"

"It's just a feeling. But he's still got to be in there somewhere. He just has to be."

Elizabeth's eyes went wide. "If that's true Carson, then we have to get John back as soon as we can. Otherwise, I'm afraid we're just going to be left with his body. And I can't have that. I am not going to let John die. Not on my watch."

**TBC in Chapter Thirteen….**

* * *

**A/N:** Not really a cliff hanger per se, but a good place to leave it. Then you won't be chomping at the bit so much to find out what happens next. Hope you enjoyed. I'll write soon. Later days. :)


	13. Chapter 13

I don't own SGA or any of it's characters. I only own the badguy and my story, with a few extras thrown in there for good measure. Hey there ya'll! I was able to write another chapter. I guess I don't have writer's block yet. It seems to be flowing out of me because I am in the midst of writing another one too. I may or may not get that one uploaded tonight. But have fun with this one. Later. And thanks for the reviews. :)

**Chapter Thirteen**

As night slowly crept up on the floating city of Atlantis things seemed relatively quiet. Colonel Sheppard and Ronan Dex, along with a few other patients, lay unmoving in their beds. The low level lights were on and shadows danced around the room as infirmary personnel moved about. In the Control Room situated in the centre tower, a skeleton crew of technicians kept watch over the Stargate while Dr. Elizabeth Weir wiled away her hours in her office, thinking about her crew in the hospital wing and trying to keep her mind occupied. It wasn't working very well. There were only so many computer games to be played and she was almost beyond bored with all of them. Waiting for any news about the operation of the pods in the lab was driving her crazy. And she hated the fact that she was not in the least bit tired. It was a good thing that the sun had only set less than an hour before or she would have felt guilty about staying up late. In the lab situated in the lower levels of Atlantis, Dr. Rodney McKay and Teyla Emeggan were busily trying to get the pods to work that would help Colonel Sheppard get rid of the burden in his mind called Puren. It was not going as fast as they would have liked. Rodney was ever steadily becoming more and more frustrated, which in turn meant that he was getting even more annoying to Teyla. As well as rude. The physicist could just not help it. It was the way he was wired. And the fact that he kept complaining about his back made the Athosian woman want to throttle him. Teyla, for her part, tried to remain in good spirits but it was extremely hard. She knew they were doing this for John so she kept her mouth shut the best she could. But there were instances where she could not help it. Where she just had to voice her opinion to Rodney. All he seemed to do was rant. So maybe in the depths of the city things were not all that quiet. Dr. Carson Beckett had fallen asleep at the desk in his office. His head was resting on his folded arms which were on the desk. He could no longer keep his eyes open. His staff just continued to work while they let the man sleep. They would wake him up if anything happened. Things were quiet. Or so they all thought at the time. They were in for a rude awakening. In more ways than one.

* * *

"Oh that's just great!" Rodney said with a pissed off undertone. "Where the hell did that sub-routine come from? That wasn't there a moment ago." His eyes squinted in anger and he pressed a few more buttons on his data pad.

"Is there a problem Dr. McKay?" Teyla asked as she came around to stand in front of him on the other side of the console.

"What do you think? Of course there's a problem." He said without looking up from his data pad. "Every time I seem to be getting somewhere something else pops up and gets in my way."

"What is it this time?" she said placing her hands on the console in front of her.

"Some sub-routine just came out of nowhere and booted me out. Now I have to figure out what its purpose is and try to bypass it." He said sighing. "Why can't Ancient technology just be simple? And why the hell don't they have instruction books? I mean 'Ancient Technology for Dummies' would have been perfect here."

Teyla cocked her head to the side indicating confusion. "What do you mean Ancient Technology for Dummies?"

Still not raising his head to look at her he said, "It's a series of books back on Earth. You know, 'Computers for Dummies', 'Cooking for Dummies', etcetera, etcetera? There are all sorts of them. It's just a lamens way of explaining things to people. A kind of instruction book if you will. Get it?" He continued to type.

"I believe so." She said as her mind worked in overtime.

"Good, good. Very good. Now please let me finish what I was doing." He said with a hint of anger.

Teyla just creased her brow and returned to what she had previously been working on. Throttling the man was still on her mind.

* * *

Ten minutes later Teyla heard something come out of Rodney's mouth that she knew she had not wanted to hear. That she had been dreading to hear. Two words so simple in their connotation… "Uh oh."

She turned towards him and saw the look on his face as he continued to stare at his data pad. It was fright. "What is wrong Rodney?"

He did not answer right away. When he finally did his words spoke volumes. "I think I just created a feedback loop. We have to get out of here now!" He unhooked his data pad, grabbed hold of Teyla's arm and took off running for the door.

Teyla just obediently followed him, knowing full well the implications in what he had just said to her. Nothing else was said between the two as they raced for cover. They had just reached the confines of the lab at the end of the hall when they heard an explosion emanate from where they had just been. They both ducked but they had been safe where they were. When the noise had died down Rodney slowly stepped out in to the hall with Teyla at his side. They stood for what seemed like an eternity while they stared at the entrance to the lab where the pods were. This was so bad.

* * *

In the Control Room, the technicians were surprised when they felt the city shake. They all looked around confusedly. Elizabeth came running out of her office. "What was that?" she asked as she came to stand beside the tech that sat by the DHD.

"Unknown Ma'am. We're checking on it now."

Instinctively she looked at the Stargate but it just sat there idly mocking her.

"There was an explosion on Sub-Level Three. I believe it's the area where Dr. McKay and Teyla are working." The tech said with a hint of fear in his voice.

Elizabeth immediately tapped the com in her ear. "Rodney? Teyla? Are you there? Can you hear me?" She was relieved when she automatically heard a response to her barrage of questions.

"We're here Elizabeth. We were able to get out before the explosion. We're both okay." She heard Rodney say in a shaky voice.

"What happened? What exploded?"

"A new sub-routine cut me out of the program and when I tried to bypass it I created a feedback loop and a few of the pods exploded. We managed to get to the lab at the end of the hall before they exploded."

She could hear things being moved out of the way as Rodney spoke over the radio. "Have you managed to get back in to the lab yet?"

"That's what we're doing now. We're going to have to get back to you after we've been able to assess the damages."

"Do you think we'll still be able to use the pods to help John?" she asked worriedly.

"I sure hope so Elizabeth, because if we can't then I have no idea how we're supposed to help Sheppard."

"Do the best you can Rodney. I'll be waiting for your update."

"You'll be the first to know Elizabeth."

She sighed in resignation and tapped her com off. Then she turned and faced the tech that sat beside her. "Let me know if you come across any other problems. I don't care how small you think they are. I want to know."

"Yes Ma'am." He said with a nod.

She slowly turned and headed back to her office. How could anything else get worse. If it wasn't one thing then it was another. And it all started because a certain pig headed Colonel wouldn't tell anybody that he had the flu. When he got better she wasn't going to let him forget this. This was something that she could hold over him for a long time to come. She liked leverage. She smiled lightly at the thought and could just see John smiling at her with that lop-sided grin of his saying 'how was I supposed to know a megalomaniac Ancient device would try to take me over. I was sick after all.' She could read him like a book. If she were a betting person she would bet her life savings that something close to those very words would come out of his mouth. She smiled again and then decided that she would head down to the infirmary and see how John and Ronan were doing. She wanted to do something besides sitting around in her office doing nothing.

* * *

In the infirmary John's eyes slowly opened up. He did not make a sound as he looked around the room. He spotted Ronan lying in a bed not far from his left. Then he saw two Military personnel lying further on his right. He was extremely confused. He tried to move his arms but could not. He looked at his left arm and saw that it was restrained to the bed. He became even more confused. He turned his head to the right when he heard somebody come into the room. It was a nurse. She seemed to be heading towards Beckett's office. At first he had wondered why he had woken up. Then he remembered feeling that something had happened to Atlantis. So he had forced himself to wake up. Pushed Puren to the back of his mind for the time being. It was hard to keep him there but he was managing for the moment. He licked his dry lips and spoke. "Hey?" he said and coughed when it came out as a whisper. He closed his eyes for a moment and then tried again. "Hey?"

The nurse stopped abruptly in her tracks and turned around. When she spotted John wide awake a large smile formed on her face. She quickly walked over to him and leaned over him slightly. "Is that you Colonel Sheppard?" she asked.

"Ya. It is. I need to speak to Dr. Beckett." He said hoarsely.

"I'll go get him for you." And with that she hurried off to his office.

Within minutes both Beckett and the nurse were at his side. "Well now Colonel, it's nice to finally speak to ya. How did you manage to push Puren back?" he asked as he took John's pulse.

"It's very hard. He's there at the edge of my mind trying to get back. I don't know how much longer I can keep him there. I felt something happen to Atlantis. What happened?" he asked and then winced with pain.

"There was an explosion in a lab. Rodney and Teyla were there but they were unharmed thank god. Rodney just seems to keep babbling about needing instruction manuals. Teyla's on the verge of killing the wee bugger if he doesn't stop complaining about that and the pain in his back and wrist."

"Puren hurt Ronan didn't he? It was like a blurry afterimage. I could faintly see him doing something to Ronan but I wasn't sure what exactly. Every time he attacks somebody that happens. And it's even worse that I can't stop him. Can't stop myself. I hope you guys figure something out soon because I don't know how much more I can take of this." he swallowed and then winced again.

"Just try to hold out John." Came a familiar voice from behind Beckett. When Elizabeth came in to view John smiled slightly.

"I'm trying my best Elizabeth. But it's just so hard. I'm able to keep him away from certain intel but he's going to get to it eventually. Then he'll know all there is to know about Atlantis. That can't happen. And I'm just wondering why you haven't brought Zelenka into all of this? Rodney and Radek would make an unbeatable combination. Am I missing something?"

"John, Radek is still off world with Major Lorne and his team. Remember? They've been on PFJ-468 for the last four days, trying to set up the communications outpost."

John blinked and then he suddenly remembered. "Oh yeah. Radek was complaining that it should have been Rodney going and not him. That he was not meant for off world missions. And if I remember correctly there were a few choice Czech swear words sent Rodney's way."

"You remember correctly John." Weir said with a smile. "He was one of the most unhappy people I have ever seen. I think he's still mad with Rodney over that incident with the children where he came back with his hair in ties and makeup on his face. He wouldn't speak to Rodney for days after that."

The pilot chuckled as he remembered the incident and then closed his eyes in pain as he tried to keep Puren at bay. He was scared. So scared. But he didn't want to let the others know exactly how he felt. Although they could probably figure it out for themselves. He was in too much pain to keep a lot of his emotions to himself.

"Are you alright Colonel?" Beckett asked as he placed his hand on the man's right arm.

He received no answer for several minutes and then John seemed to collect himself and he opened his eyes. "Yeah. I can feel him nudging away in there. It's really starting to grate on me Carson. Get this freak out of me as quickly as you can please. Or I'm going to try and find a way to do it myself." The intonation of his voice let them know just how serious he was about the latter part of his statement.

Carson and Elizabeth glanced at each other and then looked back at the Colonel. "We're doing our best John." Weir said. "We've just run into a snag right at the moment. But I'm sure that Rodney will be able to fix it. You know him."

Sheppard sighed and then looked at the ceiling for a moment. When he turned back to Elizabeth he had a slight look of resignation on his face. Then it was gone. "Yeah, I know Rodney. Too well if you ask me. But I get what you're saying. If there was anyone I could trust with something like this, Rodney is it. But please don't tell him I said that. Either of you." He said as he looked from Weir to Beckett. "I don't want his head to explode from how big his ego will become."

Weir and Beckett both laughed at the sarcastic comment. It sure sounded like their Colonel Sheppard. The one person who could stand up to Rodney with stinging sarcasm. "Don't worry John. He won't hear it from us. Will he Carson?" Weir said as she glanced over at the doctor on the other side of the bed.

"Not a word Colonel. Cross my heart and hope to die, stick a needle in my eye." Beckett said as he tried to keep the amusement out of his voice.

Sheppard could barely keep in the laugh. His lips were pressed tight together. Then he could no longer suppress it and he laughed heartily. The nursing staff were completely confused at why the head staff of Atlantis was laughing so hard at a time like this. They shook their heads and continued on about their business. The three expedition members just continued to laugh, their faces slowly turning red.

**TBC in Chapter Fourteen….**

* * *

**A/N:** Hope you liked this one. And I didn't leave it as a cliff hanger. I just wanted to end one of my chapters on an up note. And it shows that Sheppard is still there and so is his sense of humour. But that probably won't last too long because you know who is still around waiting to cause even more havoc. Chow. Later days folks. :)


	14. Chapter 14

I don't own SGA or any of it's characters. I only own Puren and some of the extras. Hey there folks. Sorry it's been a few days, but I was finally able to write this chapter. Thank you for the new reviews. This is a bit of a short chapter, but you never know, the next one could be longer. I've already started writing it. So enjoy the chap. Ta. :)

**Chapter Fourteen**

"Well this sucks!" came the sudden comment from a corner of the debris strewn lab. Rodney stood up slowly from his crouched position and unconsciously rubbed his lower back.

Teyla looked at him from across the room. "What problem have you found know Dr. McKay?" she asked as she brushed a piece of hair away from her face.

"These two pods are completely ruined." He said as he threw his arms up in the air in complete frustration. "Damned Ancient technology."

"What about the other two pods?" she asked as she moved towards him. "Are they still working?"

"Well that's debatable. They should be working because they worked through that console over there and not through this one which caused the feedback loop. But they're not. There's something here that we're not seeing. That I'm not seeing. And yes, I'm admitting that freely. Just don't tell Sheppard or Ronan or I'll never hear the end of it." He said looking at her as she approached him. "Don't give me that look. You know what I mean. As soon as they hear that I'm admitting to any kind of defeat they'll bug me day and night. You know I'm right."

Teyla just stood with her arms crossed and her left eyebrow raised, staring at him in consternation. Rodney, unable to take the staring, self-consciously turned around and picked his data pad up off of the floor. He made a comment in his head but did not have the courage to voice the word to the Athosian. He knew he would get his ass kicked for it. Plus he knew that he really didn't feel that way about the woman so he pushed the thought out of his head and turned back to her. She had an amused smile on her face.

"What?" he said as he stood there and looked at her.

Her smile broadened and then she spoke. "You are worried for Colonel Sheppard and Ronan. It is nice to see you reacting this way. It is comforting."

"How am I reacting?"

She smiled and then turned away from him, letting him figure things out for himself. The man may have been an overbearing egomaniac, but he did care for his friends. And at least that was breaking his self absorbed attitude.

"Teyla! How am I reacting?" he said again as he watched her walk away. When she didn't answer him he frowned and then stood in place trying to figure out what she had been talking about. When he finally got it his features brightened and it was as if a light went off in his head. "Oh. I get it! I get what you mean! Thanks." And with that said he quickly went back to work without saying another word.

Teyla turned and just shook her head lightly, a smile plastered on her face. Rodney was definitely an interesting person to work with. One of a kind. And she wouldn't have it any other way.

Weir walked into her office and slumped down in her chair, resting her arms on the desk and then she put her head down on top of them. She was exhausted. She had laughed so hard with Beckett and Sheppard that she was having a hard time keeping her composure. It had been exhilarating to do that, especially knowing what lay just below the surface in John's mind. It hadn't lasted as long as she had hoped it would. Shortly after the display they gave to the infirmary staff, Puren seemed to rear his ugly head. John had almost immediately stopped laughing and he had grimaced in pain. 'I do not believe this is a prudent way of using my time Elizabeth Weir.' She had hated hearing those words coming from the mouth of John Sheppard. She, herself, along with Beckett had stopped their own laughing and had stood up as straight as their frames would allow them. Then the pilot had abruptly passed out. He could no longer keep the evil in the recesses of his mind. She knew that it meant that Puren was getting stronger and that they had to get the pods working as fast as they could. She had a gut feeling that it was only a matter of days before the Ancient device would take him over for good. A tear came to her eye and she sniffed her nose. She was so scared.

Elizabeth hitched her breath when she heard a knock at the door to her office. When she lifted her head up from her desk she saw Rodney and Teyla standing in front of her. She straightened immediately, knowing that they would have some kind of news for her… whether it was good or bad.

"I'm sorry Elizabeth, did we wake you?" Rodney asked as he stepped inside her office.

"Not at all Rodney." She said wiping the tears away from her eyes with her fingers. "I was just thinking. Please, come in and sit down." She gestured to the two chairs sitting opposite her on the other side of the desk.

Rodney and Teyla sat down across from her and waited until she composed herself before they mentioned what they had found. The head of Atlantis was looking extremely tired. They wondered if she had been getting any sleep. They doubted it. She probably wouldn't get much. At least not while John and Ronan were in the infirmary and John was so close to being lost. Naturally she was upset.

"Well, what have you found out about the pods?" Weir asked as she steepled her fingers in front of her.

"Two of the pods are completely destroyed Elizabeth." McKay began. "The feedback loop and the resultant explosion ruined them. There's absolutely no way that we can get them or their connecting console to work again."

"What about the other two? What did the explosion do to them?"

"We are having a hard time getting them to work Dr. Weir." Teyla broke in before McKay could say anything. "We are trying our hardest but it would seem that the two that were destroyed were the only ones that had been initialized." The Athosian looked to Rodney to finish the thought.

McKay nodded. "We weren't sure at first why the other two weren't working. They were safe from the explosion but they were dead. I knew we were missing something, but I couldn't figure out what. Then Teyla innocently asked if the power was correctly connected to it and the pods. I felt so stupid because I wasn't thinking in that direction. I didn't think of the batteries."

"So it was an internal power source that hadn't been initialized by the ATA gene yet?"

"Correct." He said as he caught Teyla's confused glance out of the corner of his eye.

"But you have the gene Rodney. Why couldn't you just activate it yourself?" Elizabeth asked.

"Unfortunately, I think it requires the touch of a natural gene. Not a fabricated one. That had to have been something the Ancients came up with. Maybe so that nobody but a natural Ancient could use them. Who knows."

"So how do you expect to get the pods going Rodney? There are only so many people here on Atlantis with the natural ATA gene. John would normally be the one to ask… but well… you know. And Major Lorne is off world with Zelenka. His gene is not as strong as John's… well, nobody's is actually. But it's strong enough. Who are you going to ask to initialize it?"

Rodney thought about it for a moment and then it came to him. "The only one I trust enough for something like this, being that both Colonel Sheppard and Major Lorne are unavailable, is Carson. I know he has a way of letting things get a little out of control when he tries to activate things, but I wouldn't ask anybody else. What do you say Elizabeth?"

Weir smiled. "I totally agree with you Rodney. I wouldn't have it any other way. Do you want me to ask him, or do you want to?"

"Um… if you wouldn't mind asking him…?" he let the question hang in the air.

"You really don't want to go to the infirmary, do you?"

"Not particularly, no. At least not right now." McKay said with an air of self-consciousness. He lowered his head and started to pick at a loose thread that was sticking up on his jacket.

"No, I don't mind Rodney. I get it. I don't want to see him that way either. I'll talk to Carson as soon as we're done here. Okay?" she said with a guarded smile.

McKay slowly nodded his head and then he stood up, Teyla following suit. When they came to the door of the office McKay turned around and looked sadly at her. "Thanks Elizabeth."

She nodded her head and then watched the two teammates walk out of her office. It had been a long time since she'd seen that look on the physicist's face. She watched them until they had disappeared from view and then tapped her ear piece. "Carson. Can I meet you in your office? I need to discuss something with you."

She heard is Scottish brogue almost instantly come over the air way. "Yes, of course Elizabeth. I'm here now. I've been keeping an eye on the Colonel and Ronan."

"I'm on my way. I'll be there shortly."

"I'll be waiting."

She tapped off her earpiece and then stood up from her desk. As she headed out her door the thought of getting their Military Commander back came flooding through her mind. This would work. She knew it would. It was gut instinct. A brief smile flashed across her face and then it was gone.

**TBC in Chapter Fifteen….**

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**A/N:** So, what do you think Beckett's response will be? Will he say 'yes' or will he say 'no'? You'll have to wait until the next chapter to find out. Hehe. Sorry. Anyways, hope you liked the chapter. Later days folks. :)


	15. Chapter 15

I don't own SGA or any of it's characters. My story and Puren are what I own. Hey there folks. I tried to upload this stuff yesterday but it just wouldn't let me. I don't know if you had the same problem. Anyways, here's the new chapter. I think I'm on a role with this story. I have so many things in mind. Have fun reading everyone. :)

**Chapter Fifteen**

When Elizabeth arrived at the infirmary she slowed down when she came to Sheppard and Ronan's sides. She stood in between the two beds and looked from the Runner to the pilot. She sighed and then turned towards Carson's office. When she entered she saw the man sitting behind his desk reading files. "Thank you for meeting with me Carson. This is important."

"Not a problem Elizabeth. Please, have a seat." He gestured to the chair which sat on the other side of his desk.

She smiled and sat down on the edge of the chair. She placed her elbows on the desk and put her hands up to her chin. "Carson. I need you to do something for me. And I need you to do it right away. And please think about what I am asking of you before you answer." She said with an imploring look on her face.

"What is it that you require of me Elizabeth?" he asked curiously as he moved forward in his chair.

"I would like you to go down to the lab where Rodney and Teyla are working on the pods. They need you to initialize them. They said that a natural ATA gene is required to activate them before they can be used. And since John and Major Lorne are unavailable, you are the only one we trust with this duty. What do you say Carson, will you do it?" she asked with bated breath.

"Yes." Beckett said without hesitation. "I'll do it."

Weir paused for a moment having not expected the answer that she had received. "You said yes."

"I know what's at stake Elizabeth. I'll do anything to help get Colonel Sheppard back with us. And if that includes me having to activate some Ancient doohickies, then yes, I'll do it." Beckett said with a grave smile on his face.

Weir clasped her hands together and smiled. "Thank you Carson. I guess you do know what's at stake." She let her gaze wander out to where Sheppard and Ronan lay. "How are they doing?"

"I expect that Ronan should be waking up soon. He's doing better. The Colonel is a completely different story as you well know. I've had to keep him sedated so that Puren will not be able to use him. I hate seeing the lad in restraints. This whole thing sickens me. It really does."

"I know what you mean. It's not something that anybody should see. Their friend tied up on a bed." She sighed and turned back to him. "Rodney and Teyla are waiting for you in the lab. The sooner you could get there the better."

"I'll go as soon as I've talked with my staff. Tell Rodney and Teyla that I will be there within the next twenty minutes."

"Very well." She stood and faced the doctor. "Thanks again Carson. This will help a lot." He smiled and she turned and walked out the door. He could see her walk out and stand between the two men laying prone in their beds. She placed her left hand on Ronan's right arm and her right hand on John's left arm. She bent her head slightly and he knew that she was praying for them. Then she was out the door of the infirmary and out of sight.

* * *

Almost twenty minutes later Dr. Beckett arrived in the lab where the pods were. True to his word to Weir. "I'm here Rodney. What do you need me to do?"

Rodney's sweaty head popped up from under the control console to the pods and stared at the Scottish doctor who stood in front of him. "You're here!"

"Of course I'm here Rodney. I said I would come." Carson said as he walked towards the man.

McKay stood up and wiped his hands on his pants. "I just didn't think that you were going to get here so fast."

"Well I'm here Rodney. What do I have to do to help Colonel Sheppard?"

"Ah yes. Come over here Carson." He said as he held up his arm to guide the man in his direction. "I need you to use that ATA gene of yours and touch this thing."

Beckett walked over to where Rodney and Teyla were standing and stood beside the mentioned console. He looked at the two members of SGA-1 with a hesitant face. He knew he had to touch it for the Colonel, but he still hated to touch the bloody things after what had happened in Antarctica. He had accidentally set that drone on Colonel Sheppard and General O'Neill and almost killed them. That had been a bad experience. He reluctantly held his hand out.

"Come on Carson. What are you waiting for?" McKay asked with his brow furrowed. "Just touch it and then we can get down to business."

"Right." Beckett said and then placed his right hand on the top of the console. He watched as it came to life, lights flashing.

McKay's face lit up like a Christmas tree and he clapped his hands together in front of his face. "Brilliant Carson!" He moved forward and placed his hands on the console, trying to figure out what to start with first.

Teyla moved to stand next the doctor and watched her teammate. He was enthusiastic to say the least. They watched him systematically go through every control with a giddy expression on his face. "Did it work Dr. McKay?" Teyla asked.

"Hmm?" Rodney said distractedly.

"Did it work?" she asked again.

McKay looked up at his two friends with his eyebrows raised. "What was that?"

"Did it work?" Teyla asked for a third time, more frustration in her voice.

"Yes. Yes. Of course it worked. Now you can get back to your voodoo Carson." He said as he basically shooed the doctor away.

Teyla and Beckett looked at each other and then the doctor threw his arms up in the air and walked out of the lab. He knew he wasn't going to get any kind of a 'thank you' from the physicist. But at least they were going in the right direction. The pods would work now. That's all that mattered.

* * *

John's head twitched and then moved to the left. His eyes were closed and it looked like he was dreaming. In reality, Puren was trying to wake the pilot up. Trying to control his ever thinning body. He began to twitch more and he began to breath heavily.

Daylight had already come to the Lantean home world but the infirmary had been kept on a lower lighting level. Ronan's eyes slowly began to open up when he heard the moaning coming from his left. He blinked numerous times and then turned his head to face the noise. He was surprised to see Colonel Sheppard laying just over from him. He coughed when he tried to swallow and then reached his hand up to his throat. He rubbed the offending bruises and then winced with pain. He slowly began to sit up in the bed and then sat and stared at his commanding officer. He placed his hands on the bed on either side of him and then looked at the floor. When he finally managed to get himself up off of the bed he swayed slightly and then reached out for Sheppard. He placed his left hand on the Colonel's arm and then stood over him. "Sheppard. Are you there?" he asked in a raspy voice as he lightly shook him.

The Colonel continued to moan and twitch as the Runner tried in vain to wake him up. He wasn't even sure if it was Sheppard that he would be waking up. He had remembered the force which Puren had used to bring him down and for the first time had realized what a threat the creature actually was. Not just to the pilot, but to him and his new found team as well. Then quite suddenly the prone man's eyes opened and he was breathing quite rapidly. Ronan did not like what he saw.

Within those bloodshot, tired hazel eyes was evil. Not the Sheppard that he had at first reluctantly decided to get to know, but pure evil. Puren. He backed away from the restrained hands of the man. "How is your neck Ronan Dex?" came the taunting, familiar voice. The Runner touched his neck without even realizing it.

"It's fine." He said with an even raspier voice than usual.

"Is it now?" the body of John said with a malicious smirk. "Then why are you touching your neck? Does it hurt?"

Ronan brought his hand down and frowned. "I know what you're trying to do and it won't work."

"Nice bruises." Puren continued. "It is nice to know that this vessel is physically strong. It will make my job much easier."

Ronan growled. And if anybody else had been there they would have thought that it sounded even scarier than it normally did. The man was about ready to reach over and wipe the smug smile off of his friend's face. But he knew that would only hurt Sheppard so he refused to give in to the being's goading. "We'll defeat you Puren. It's only a matter of time."

"I highly doubt that Ronan Dex. This vessel will be mine to command and there is nothing that any of you can do about it."

The frown intensified on the Satedan's face and he turned when he heard someone approaching the infirmary. He was not surprised to see Beckett appear at the entrance to the room. Carson stopped in his tracks when he saw the Runner. "Ronan. You're awake lad. I'm glad to see it. How are you feeling?"

"Not now." Came the raspy voice as he pushed by the doctor. "Take care of Sheppard. I need to see Weir."

Before Carson could object his patient was out the door and on his way to the Control Room. He shook his head and turned to see that the Colonel was awake as well. "Hey lad. Good to see you up."

"There is nothing that Dr. Elizabeth Weir can do to help. I will have this vessel."

Beckett sighed. "Not you again." And then he turned and left the room, Puren spouting his regular bull the whole way to his office.

**TBC in Chapter Sixteen….**

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**A/N:** Well, how are ya likin' it? I'm likin' it, so I hope you are. I have another chapter to post after this but I'm afraid I have to write more after that. Anyways, Enjoy the next chapter ya'll. Later Days. :)


	16. Chapter 16

I don't own SGA or any of it's characters. I only own my badguy and my story... with a few extras thrown in for good measure. Well, I'm living up to my word folks. I'm posting another chapter. But this is all I have written at the moment so I won't be posting another one tonight. So have fun. :)

**Chapter Sixteen**

Expedition members jumped out of the way when they saw the Satedan striding down the hallway still wearing the burgundy scrubs from the infirmary. As soon as they saw the determined and pissed off look on his face combined with the speed at which he was walking, nobody had wanted to get in his way. That was something they didn't want… to be decked by the one person who could do them considerable harm. Even above Teyla. They had gotten to know the Runner, as much as anyone could, but they were still quite jumpy when it came to the man. He was one scary dude… even on his good days. Which they couldn't tell the difference. So they just continued to avoid him.

When he arrived at the Control Room, nobody objected that he wanted to see Dr. Weir. They just let him go. He barely even knocked as he entered the room. "Why hasn't McKay fixed Sheppard yet?"

Elizabeth looked up at the man. He looked horrible. Pissed and horrible. Bad combination she thought. "Direct as ever Ronan." She said without even a hint of a smile. Neither of them were in that kind of a mood.

"Answer my question. Why hasn't McKay fixed Sheppard?" He stood directly in front of her desk and crossed his arms across his chest. He looked extremely imposing.

"There was an explosion Ronan. It ruined two of the pods. It took some time, but Rodney, Carson and Teyla managed to get the other two working. Now Rodney and Teyla are trying to make sure that the pods are safe to use. Safe to put John in. It shouldn't be much longer." She didn't know why she felt the need to explain everything to the Runner. She didn't have to. It was her discretion about what information she gave out. But the man had become a close friend of the Colonel's so she told him everything. At least everything that she knew.

By the time she had finished Ronan was now sitting in the chair across from her. Still with his arms crossed over his chest. The bruises on his neck were turning dark purple and it was a strange sight to see. Never had she thought that he would be the one who had been beaten. It was usually the other way around. But she knew that Puren had taken him off guard and that it had been almost fatal.

Ronan just frowned at her. It was an intimidating frown. And she was a hard woman to be intimidated by anyone. Ronan was different though. Maybe it was that he was an alien. Or maybe it was because of his size. Or hell, it could have even been both. Any way that she looked at it though… he was just an intimidating force.

"I'm going down to the lab." Ronan said as he stood up.

"Do you really think that's a wise decision? You just woke up less than half an hour ago. Don't you think you should get some rest?" she asked concerned.

"I'm fine. I don't need to rest." He said determinedly.

She thought about his statement for a moment and then realized that he was probably the only person who could say that and make her believe it. Even though he _looked_ like hell it didn't mean that he was about to keel over. She finally nodded her head in agreement and watched as the man turned. "Ronan?" she said before he could leave. He just turned and looked at her with his right eyebrow raised. "Just a thought here. If you're going to the lab, can you put some regular clothes on?"

He looked down at the burgundy scrubs he was wearing and then back at Weir. "Hm." He said in what she thought was an agreement and then he left the room.

A smile finally reached her face and she shook her head. And, she wasn't sure, but she thought she caught the tiniest smile on Ronan's face as well. Or was that just her imagination? She looked at the man as he disappeared from view. "Nah." She said shaking her head. "It was a smile."

* * *

There was a clank of sound coming from Rodney's direction and then emphatic profanity. Teyla turned around from her position at the console in time to see the physicist sitting on the floor rubbing his head. "Dammit! That's going to leave a mark. Ow!"

"What happened Dr. McKay?" she asked as she came over to stand in front of him.

"I moved the wrong way and hit my head on the under side of the damned pod." He rubbed profusely at the spot and grimaced.

"Why were you under the pod to begin with Rodney?"

He craned his head up towards her and gave her one of those 'are you stupid' looks that he was a master at giving. "I was checking on the connection. What do you think I was doing?"

She crossed her arms over her chest. "It was a valid question Rodney." She said raising her left eyebrow in a frustrated manner.

McKay, with an equal, if not more of a look of frustration on his face stood up from the floor with his data pad in hand and walked past her. "We'll talk later about the validity of your questions. Right now we have to get these pods running at one hundred percent. Is that too much to ask?"

Teyla took in a deep breath as she tried not to strangle the man and then turned to follow him. When she arrived at the console McKay was already pushing buttons. She did not interrupt him.

"This should be the sequence to get the pod running at full capacity. But as I said before, it would be a lot easier with 'Ancient Technology for Dummies' at hand."

"It better be the right sequence McKay." came a deep raspy voice from behind them. When they both turned they saw Ronan standing at the entrance to the lab, wearing his brown leather pants and beige top. His long, dreadlocked, brown hair was tied back which made it quite easy for them to see the massive purple bruises that had formed on his neck. Puren, or Colonel Sheppard for that matter, had done considerable damage.

"Ronan. It is good to see you up and around." Teyla said with a large smile and gave the man a hug when he arrived at her side. He gave her a slight hug back and then stood with his arms crossed in front of his chest again.

Rodney just looked at the man, not sure what to say. Almost a minute went by before McKay said anything. "So. How are you doing?" It was lame, but it was the only thing that he could think of to say.

"Fine." Was the only word that Ronan said to answer him.

"Right. The monosyllabic answer. I can live with that. How's Sheppard?"

"Not good. He's awake, but Puren showed up. Which is why I'm here."

"Dammit. I'm moving as fast as I can Ronan." He said defensively. "It's not my fault that there's a learning curve when it comes to Ancient Technology." Ronan and Teyla both looked at him with some confusion and Rodney rolled his eyes and sighed. "Never mind. Why do I always need a translator when I'm talking to you two?" He turned back to the console and began pressing buttons.

"Listen McKay." Ronan said with an angry tone. "Get this thing working. Sheppard's fading fast. And I don't know about you, but I don't want to see him die. Even if it is just his mind and not his body."

Rodney looked at the Runner incredulously. "What the hell are you talking about! Of course I don't want to see Sheppard die! What do you take me for? I like the insufferable man just the way he is. The rakish hair, the uncalled for sarcasm, his Captain Kirk way with the ladies and yes, even the hero complex! He's my friend!"

"Then start acting like it McKay!" Ronan said using as much of his voice as he could while still trying to sound menacing.

"Excuse me!" McKay said with a loud squeak.

But before the argument could continue, Teyla stood between the two men and placed a hand on each of their chests. "Stop it! We do not have time for this childish argument!" She looked from one to the other.

They both held their tongues. Ronan's mouth looked like he was about to bear his teeth. It would have made him look even more animalistic if he had had fangs. He was breathing quite heavily. Rodney, on his part, had his lips pursed tightly together. It was obvious to her that he was trying to keep in a very nasty comment that would have been directed at the Satedan.

"Ronan." She said facing him. "Rodney has been down here almost constantly working on these pods with me since we found them. He is trying extremely hard to get them working so that we may save Colonel Sheppard. I understand that you are angry and frustrated with the situation, but you do not need to act this way with him. He is being a true friend by doing this." Ronan glanced at her and then back at Rodney. His face had softened somewhat. As much as that could be possible with him.

Teyla turned to face McKay. "Now Rodney. I know what you are doing for the Colonel. We all do. But you do not need to act so condescending towards us. You are not the only one who is trying to bring him back to us. You have to understand that I am here and I am willing to help you. And that Ronan is upset and wants to help in his own way. So please, let us just work together and save Colonel Sheppard." She looked imploringly at the man. Rodney looked at her and then back at Ronan. He nodded his head.

Teyla could see that the tension level in the room had dissipated somewhat so she took her hands down from their chests and then stood back from them. "Thank you. Both of you. Now please shake hands and agree that you are going to work together from now on to help the Colonel. No more arguments. Agreed?"

"Agreed." They both said simultaneously and then reluctantly shook hands.

"Good. Now let us get back to the task at hand shall we?" she said and then turned to face the console. She knew the day was going to be long, but at least she had been able to get her other teammates to work together. Sort of.

**TBC in Chapter Seventeen...**

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**A/N:** Have fun with this chapter? I hope so because I don't know when I'm going to get to write more. Not tonight, but maybe tomorrow. You'll have to wait and see. Later days folks. :)


	17. Chapter 17

I do not own SGA or any of it's characters. As I've said previous times I own Puren and my story. Hey there folks. Sorry it's been some days since I've posted a chapter. This is a short one but it's a fairly significant one too. Hope you enjoy. :)

**Chapter Seventeen**

As the stars began to show in the Lantean night sky the tension in Atlantis was palpable. Everyone seemed to be on the edge of their seats. The heads of the city were entering the conference room with looks of consternation on their faces. Elizabeth sat down in her usual spot and as the large doors closed the others could not decide between sitting or standing. Ronan stood leaning against the left wall with his arms crossed in front of him. That seemed to be a mainstay for him. Rodney sat down to Elizabeth's right and seemed to be staring at his hands which were wringing together almost constantly. He was nervous. Carson sat down across from the physicist and also seemed to be staring at Rodney's hands. Teyla stood with her hands on the back of a chair to Beckett's right. She was looking from person to person trying to gauge their emotions. The only person missing from their meeting was their resident Military commander. The object of their little get together. The silence lasted longer than probably necessary.

Elizabeth finally looked at her friends and colleagues and broke the silence. "So, I take it that the reasoning behind you calling this meeting is because you are finished with the repairs to the pods Rodney?"

McKay continued to wring his hands together as he looked up at her. His eyes were conflicted. "Yes. With Ronan and Teyla's help I've managed to get the two pods to their optimal operation. It took longer than I expected, but that's what you get with Ancient technology. There were so many redundancies to work through."

"So the question remains Rodney. Can we now use them to help John?" Weir asked with as much hope as she could muster.

"Yes. I believe so. I'll need at least one more hour to fine tune everything, but yes."

Elizabeth could see the excitement in his eyes but she could also see the conflict and fear. "Why do I feel a 'but' coming on here Rodney?"

McKay looked down at his hands for a few seconds and then turned his gaze back up to their leader. "But, I'm not sure what the final outcome will be if we do this. We've never used these pods before. I'm sure that we can get Puren out of Sheppard's mind but there's no saying what his mind will be like when we finish the procedure. I just want to let you know what the risks are before we do this."

Weir nodded her head slightly and kept her eyes on the man. "I understand Rodney. We all understand. Don't we?" she asked looking from person to person. She was relieved when all of their heads nodded in agreement. Especially Ronan's. "I'm sure that John would want us to at least try and get Puren out of his head. He trusts us and I don't want to ruin that trust. Are we all in agreement that this is the correct course of action for us as well as Colonel Sheppard?"

"We all want Sheppard back." Came Ronan's deep, but raspy voice. "I say we do it."

"Teyla, what about you?" she asked as she turned her head to the Athosian woman.

Teyla looked up from the table and a worried smile crossed her delicate features. "Yes. I believe that this is the right thing to do. I agree with Ronan."

"Carson?" she asked now turning to the Scottish doctor.

His brogue was thick with nerves and tension when he spoke. "Aye Elizabeth. This is the only way to keep Colonel Sheppard alive. I agree with the others."

She finally turned her gaze back to her head scientist. "Rodney, I know this is a hard decision."

"I don't want him to die. I say yes. We do it and get as much, if not all, of our friend back as we can."

Elizabeth smiled at the remark and noticed that he was no longer wringing his hands together. As she looked from person to person she realized just how close they had all become. One of their own needed their help and by god they were going to give it. Her Military commander and friend was going to come back to them. "Then we're all in agreement." She said as she placed her palms flat on the table in front of her and stood up. "We hook John up to the pod and get him back. Let's get to it."

There was only slight hesitation from her team and then they all made their way out of the conference room. The tension had ebbed and a form of euphoria had come over the quintet. An hour from now they were going to kill Puren and heal their friend. Things just couldn't get worse, they could only get better.

* * *

'Wishful thinking' did not enter any of their heads. But as things go for the Earth expedition, those two words should have become their mantra. Nothing was as it seemed and soon they would find out just how much wishful thinking would be required.

* * *

Thirty minutes later Carson, along with Elizabeth, were in the infirmary getting Sheppard ready for transport down to the pod lab. Rodney had called up numerous times over the com to let them know of his status. He would be ready in thirty more minutes as he had predicted in the conference room. The infirmary was in slight chaos as nurses were rushing around, following Beckett's orders.

They had kept Sheppard under sedation for fear that Puren would wake and figure out their plans before they were able to implement them. The pilot was also strapped to the gurney so that if he did wake up he would not easily be able to brake free as he did previously when he hurt Ronan and the others.

Carson kept a close eye on the man's vitals as he continued to prepare. Elizabeth was helping the best she could. He knew that she wanted to be there when they brought him down to the lab. She wouldn't be going anywhere. She would be by the Colonel's side throughout the entire procedure.

* * *

Half an hour went by quickly and when they received McKay's 'ok' to go ahead and bring Sheppard down they did some final scurrying around and then pushed the gurney out the door to the first transport that was big enough to carry them all. Two nurses followed Carson and Weir out the door of the transport when they arrived on the lower level of the city.

When they arrived at the lab they saw Rodney at the main console to the pods while Ronan and Teyla stood next to him with his data pad and a few other bits of equipment in their hands.

"Ah. You're finally here." Rodney said as he looked up at them. When he saw Sheppard his eyes flinched and then darted back to the console.

'He can't stand to see John like this.' Weir thought as she moved in front of Carson and headed for McKay. "So this is it?" she said as she looked around the room in amazement. "Different then I thought they would look."

"Yes, well, welcome to our saviours. So to speak." McKay said as he looked at her with a bit of trepidation.

Weir nodded her head slightly and then moved over to the closest pod. It was sticking out of the wall with the lid open as far as it would go. She placed her hand gently on it and felt how cold the grey metal was. She moved the tips of her fingers across it as she slowly walked up its length. It was so smooth. 'So this is going to save John.' She thought to herself. She looked up at Rodney from the other side of the pod. "Shall we begin?"

"Let's do it." McKay said and reached his arm out to Carson and waved his hand to motion them over.

Carson and the two nurses wheeled the gurney over to the empty pod and came up on the opposite side from where Weir stood. "Ronan lad, I'll need yer help." Carson said with his back to the Runner.

Without saying a word Ronan came over to them and helped Beckett un strap and then place the pilot inside the small pod. They took the extra straps and tied the man's hands in front of him and then tied his feet. They didn't want him to be too mobile while he was inside. When they finished one of the nurses took the gurney away and then Ronan and Carson stepped back to let Rodney do what he needed to do. They watched the man quickly work and then move back over to the console.

"Everyone stand back while I close the hatch and initiate the start up sequence." McKay said over his shoulder.

They all moved to the other side of the console and watched as the hatch closed and the pod slid into its berth in the wall. Through the glass of the lid they could only see the upper half of the Colonel. His legs as well as his lower torso were inside the wall. "Here goes nothing." Rodney said and then hit the button to start the sequence.

**TBC in Chapter Eighteen….**

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**A/N:** Hehehehe!! So I've left you hanging huh? Sorry about that, but it was necessary. Not going to post another one tonight but I will post one or two over the course of the weekend so don't fret. Hope you liked. Later days. :)


	18. Chapter 18

I don't own SGA or any of it's characters. Hey there folks. So I'm posting a couple of very pivotal chapters for you. Hope you enjoy becasue I am definitely on a huge role. This story is coming along like clockwork. Have fun. Ta.:)

**Chapter Eighteen**

There was an immediate reaction in Sheppard when Rodney hit the button. John's body bucked and it looked like he was having a seizure. Ronan jumped forward to help him at the same time as Teyla and Elizabeth. "Wait!" came McKay's anxious voice. "He's okay, it's just an initial reaction. Wait for it." The three colleagues stopped in their tracks at the physicist's words. They looked back hesitantly at the man, waiting to see if what he said was the truth. "Wait for it." He said again, nodding his head.

When they looked back at the pilot they saw that the seizure had begun to dissipate. Then he was still again. "It's working. He's asleep. Just calm down everybody." Rodney said as he looked from the console back to the pod. They all visibly relaxed after the news that the process had begun to work. They retreated to their original positions and waited to see what the outcome would be.

* * *

John's eyes flew open and he quickly sat up. He covered his eyes from the bright light and then slowly brought his hand down. He squinted and then took a good look around. When he saw that he was on Atlantis and on the floor the confusion overwhelmed him. 'How the hell did I end up here?' he thought.

He slowly pushed himself up off of the floor and turned around to see if he knew what section he was in. He was even more confused when he realized that he was in full gear. His uniform, tac vest and P-90 all there. Now he really knew that he didn't know what was going on.

He put his hand up to his ear and tapped his head set. "Elizabeth, can you hear me?" When he received no reply he waited for a moment and then repeated his question. Still no reply. "McKay? Ronan? Teyla? Beckett? Is anybody there?" He sighed with frustration when again he received no response. "Dammit! It's Sheppard! Why isn't anybody answering me?"

'That's it.' He thought. 'I'm out of here.' He looked around, found the door and headed towards it. It slid open easily when arrived at it. "Well, at least the doors still work." He said to himself. He left the room searched the immediate hallways for a transporter to take him to another level. When he found one three hallways over he stepped inside and waited for the map to come up. "Sub level three huh. How did I get here?" He found where he wanted to go and pressed the screen with his right index finger. The door closed and seconds later he arrived on the main level of the city not far from the main Control Room. When he stepped outside he was even more confused. There was nobody in the halls. He tentatively stepped outside and looked around. "Huh?"

There was not a single soul anywhere. Nobody. And that just didn't make any sense. There were always people in the hallways. There was a large contingent of Marines as well as Scientists and Doctors. Unless they had all evacuated the city. Which made even less sense.

When he arrived at the main Control Room there wasn't anyone there. No one at the controls and no one in Elizabeth's office. He ran over to the balcony overlooking the Stargate and stood with his hands resting on it in front of him. He was breathing heavily with anxiety and worry. "What the hell is going on?" he yelled out to an empty city.

* * *

Ten minutes later he was sitting in Elizabeth's chair in her office with his weapon on her desk and he was staring at the far wall. He had tried to do a check of the city to see if there were any people around but for some reason he couldn't get the main display to work. His ATA gene was functioning properly but the controls just wouldn't work for him. He knew they had to have left the city but he couldn't figure out why they would have left without him. And why couldn't he remember anything? This was all so insane. Completely insane.

He was jarred out of his thoughts by the incoming wormhole alarm. He grabbed his P-90 and raced out of Elizabeth's office. He stood at the balcony and saw that the wormhole had engaged on the Stargate. He ran back to the DHD and hit the button for the shield. Nothing happened. "What?" He hit the button again. Nothing. "Aw crap!" he said and then raced back over to the balcony. He waited for something to come through but nothing did. Then quite suddenly the Stargate shut down. He didn't know how much more confused he could be. He ran out of the Control Room and headed towards the infirmary. Just maybe there would be answers there.

* * *

Arriving at the infirmary he slowly made his way inside with his P-90 raised in front of him. With a quick recon of the room he figured out that it was empty as well. He lowered his weapon. Then quite suddenly the lights flickered and went out. When the backup lights did not come on he turned the torch on that was attached to his P-90 and shone it around the room. Things were too damn weird and now he was adding creepy to his list. He made a mental note to raid the armory when he was through checking out the infirmary.

When he reached the far side of the room he jumped and then turned around, his finger on the trigger, when he heard a noise from outside in the hall. He quietly inched forward and stood just inside the door to the left, weapon pointing to the ceiling. He knew the light he was using was a dead giveaway but he would have been blind without it. He made a second mental note to remember to pick up night vision goggles while he was in the armory.

The noise came again. This time it sounded like it was further down the hall, moving away from him. He slowly looked around the corner and then shone his light down the hallway. He didn't see anything. He came fully around the corner and stood in the entrance way for a few moments. He debated on whether to follow the noise or not and then decided against it. He needed more gear first. He moved away from the noise and headed directly for the armory.

* * *

Arriving at his destination it took him several minutes to find everything that he needed since the lights were out. Apparently over the whole city. He put a pair of night vision goggles on his head, grabbed a number of extra clips, both for his P-90 and his standard issue revolver and then grabbed three stun grenades. He hoped that would be enough because he really didn't want to have to come back and stock up again.

He turned his light off and moved the goggles down over his eyes. Everything turned green. But at least he could see. He quietly opened the door and peered out. When he didn't see anything he stepped outside and then slowly shut the door behind him. He headed back towards the infirmary since that was where he had heard the noise. He hoped that it was just one of his colleagues. That would be a lot easier to take than a Wraith or one of the Genii or anybody else for that matter.

He methodically made his way down the halls and then stopped around the corner from the infirmary when he had heard the noise again. It sounded like a rattling noise. He really wasn't sure. He looked around the corner and still didn't see anything. Which was strange because it sounded like it was practically on top of him. Now he really was getting creeped out.

He kept low and moved down the hall, ready to fire if he needed to. He stopped when he heard what sounded like somebody whispering. He stood quietly trying to listen to his surroundings. He flinched when he heard his name whispered. And it sounded like it was coming from all around him. _"Hold on John."_ He stood straighter when he heard it that time. Then he heard a crash come from the infirmary.

When he came up to the door and peered around it he could see movement, but he couldn't tell what it was. He checked his weapon for what seemed like the tenth time and then went around the corner. "Who are you?" he said as he stood with his P-90 aimed at the area of the movement. Whoever it was had his, or her, back to him. "I said… who are you? Identify yourself." When the figure turned around to face him his eyes went wide and he stepped backwards without even thinking about it. He stumbled over something that lay on the floor and fell backwards against the wall.

He lay on the ground staring up at the person who was now walking towards him in the darkness. 'How can this be? Just how the hell can this be?' he thought and everything went completely dark.

**TBC in Chapter Nineteen….**

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**A/N:** So, can you guess who Sheppard found in the infirmary? I bet you'll be surprised when you read the next chapter. And who do you think is whispering to him? I guess you'll just have to wait and see. And please let me know what you think. I really want to read your reviews. Later days folks. :)


	19. Chapter 19

I don't own SGA or it's characters. I own my story and my bad guy. So here's the next chapter. And wait until you see who Sheppard found in the infirmary. Again, this is a pivotal chapter. A lot happens in this one. So read on and have fun. Ta. :)

**Chapter Nineteen**

When Colonel Sheppard woke up again he was surprised to see that the lights were back on. Had he imagined the whole thing? Was he still in the infirmary on Atlantis? He slowly reached up and pulled the night vision goggles off of his head and then let his hand drop to the floor beside him. He sighed heavily and for the second time that day he pushed himself up off of the floor. He looked up and realized that he was facing the door to the room.

"Nice to see you awake Sir." Came the all too familiar voice from behind him. He froze for only an instant and then slowly turned around. The pilot found himself staring at the mutated face of Lieutenant Aiden Ford. "Didn't think you'd ever wake up." Ford said with a smirk.

"Ford." Sheppard said as he stood as straight as he could. "How did you get into the city without anyone noticing?"

"Look around you Sir." Aiden said as he raised his arms up and gestured around the room. "It wasn't very hard."

"What did you do to them?" John asked.

"I didn't _do_ anything to them. Atlantis was like this when I got here. I am surprised to see you here though. What, did they leave you behind? That wasn't very nice of them."

Sheppard glared at his former Lieutenant, dressed in his rather Athosian like garb. He did not need this. Especially not from Ford. "Yeah. I guess it looks that way. Why are you here? Trying to get more enzyme from Beckett?"

"Something like that Colonel. But I guess I have the pick of anything I want don't I?" the young man said as he moved closer to the pilot.

"You'd think that, wouldn't you Ford. But I'm still here to defend Atlantis. And I'm not going to let you do anything to her." He said as he reached for his P-90. When he reached down and got air he realized for the first time that he did not have any of his weapons. 'That's just great!' he thought.

"Sorry Sir. I had to take away your weapons. Didn't want you to do anything that you would regret."

"How very noble of you Ford." John said with a slight sneer.

Ford smiled at him and then began to circle him. "I don't see how you, being just one man, will be able to defend all of Atlantis. I mean, I know you're a great fighter, but you're still just one man. And might I add… a weaponless man."

"Thanks for the reminder." Sheppard said as he watched Aiden walk around him.

"Hm. Always the comebacks. The sarcasm. It's a pity that McKay isn't here. We'd just have a fun ol' time with the witty comebacks. Can't you talk seriously for two minutes Sir?"

"Oh, I'm serious Lieutenant." He said with an edge to his voice. "You wait and see just how serious I am."

"That's more like it Sir. That's what I want to hear. So why don't we get out of here and go to the Control Room." He said as he made his way to the door.

"And why would I want to do that Ford?" he asked as he turned to face the man.

"You can stay here if you like. But I'm going to the Control Room." And with that said Aiden left the Colonel standing by himself in the infirmary. A few seconds went by. "Aw crap!" Sheppard said and then raced out of the room after Ford.

* * *

When they arrived at the Control Room Aiden headed straight for Weir's office and sat down at her desk, leaning back in the chair and putting his feet up on the desk, crossing them. He placed his hands behind his head. There was a smile plastered on his face. "I knew this was a comfortable chair."

Sheppard stood on the other side of the desk with his arms crossed in front of him. "Why did we come up here Ford? So you could sit in Weir's chair?"

"Do I have to explain everything to you Colonel?" the man said smugly.

"I guess you do Lieutenant." He said with a pissed off tone. "Now are you going to explain what you're doing here or not?"

"I thought it would be self explanatory Sir. But I guess not. I want to come back to Atlantis."

Sheppard just stared at him with his brows furrowed. He thought about that statement for a moment. "Now you want to come back? After all this time and after everything you've done?"

"Yes I do. I feel I can fight the Wraith better from here than from out there. Don't you want me to come back?" he said as he brought his feet down from the desk and sat forward in the chair.

"Not if you're lying to me. No I don't." he said shaking his head.

"I'm not lying to you Sir. I've changed my mind. Isn't that allowed?"

"You know Lieutenant… six months ago I probably would have said yes to you. But I know you're lying to me. So the answer is no. You can't come back. You're considered MIA here as well as back on Earth. And that's the way it's going to stay."

"I thought you would have been a little more understanding Colonel." Aiden said as he stood up.

Sheppard leaned forward and placed the palms of his hands on the desk in front of him. He looked up at the man. "I'm sorry to disappoint you Ford. But you're not going to get me to change my mind. So give it up."

A flicker of hate came across the Lieutenant's face and within an instant he was jumping over the desk, lunging at the Colonel. To his utter surprise, John stepped back and did not have time to get away from the man.

They landed on the floor, Ford on top of Sheppard. Aiden began to hit John and he tried to fight back. He managed to get a hold of Ford's arms but the man just kept on coming. They rolled on the floor trying to hit each other and then Sheppard managed to get the younger man in to a head lock. "What the hell are you doing Ford!" he yelled.

"You never liked me Colonel. Never." Came the raspy, stuttering voice. The man was trying to pry Sheppard's arm away from his throat.

"Here we go again. You know how many times I've had to here that crap come out of your mouth? I'm sick and tired of it. Get a new line Lieutenant." He said with anger.

For those remarks Sheppard received an elbow in the gut. The breath ran out of him and he let go of Ford. The young man stood and turned to face his ex-superior officer. "How can I get a new line Colonel when it's the truth!" he said and lunged for the pilot again. Sheppard managed to get his feet up and fired them at the man's stomach. He pushed the man away from him and Ford stumbled backwards. Then he realized, just a moment too late, that Aiden was falling towards the desk.

He watched in horror as Ford's head cracked on the side of the desk. Then the man fell limply to the floor. Sheppard was on his feet in an instant and ran to Ford's side. He checked his pulse and couldn't find it. His mind was racing. "No! No! No!" He still couldn't find the pulse. "Godammit! You can't be dead!" Tears were starting to flow down his cheeks. He didn't even realize that he had begun to cry. He felt numb inside as he continued to try and revive the Lieutenant. After many failed attempts at CPR he sat crouched on his knees, his hands resting on the prone man's chest. He began to shake his head, then stood up and walked slowly over to the door. He was breathing quite heavily, almost to the point of hyperventilating. He turned and faced the dead Lieutenant. Then his legs gave out from under him and he collapsed to the floor. He sat there numbly, bent over with his face in his hands. And he began to sob.

**TBC in Chapter Twenty….**

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**A/N:** So were you shocked? Did Ford even enter your minds? What do you think will happen now that Sheppard has killed his friend? A lot of questions, I know. And I've left you all hanging again. But isn't this a great place to end a chapter? Later days folks. :)


	20. Chapter 20

I do not own SGA or any of its characters. I own my story and my bad guy. Hey folks. Here I am again. Writing more. I'm glad you liked the last chapters. I love how this is going. And there's not going to be much left. Just to let you know. Getting near the end. So have fun with this one because there are some things that are answered. Later. :)

**Chapter Twenty**

John sat crouched in the corner of Elizabeth's office staring at the body of Lieutenant Aiden Ford. He had lost all track of time. Did not realize how long he had been sitting in the position he was in. His whole body felt numb and the tears were drying on his cheeks. Every now and then a stray tear rolling down. He had killed a friend. Someone he had used to trust until he had been infected by the Wraith. How could he live with himself? With the knowledge that he was capable of this? That kind of thought had been unimaginable until it had actually happened.

"_Hang on John. Hang on. You'll be free soon."_ He flinched when he heard the whispered voice again. He blinked his eyes and looked around the room. Again it had sounded like it was all around him. _"I know you can hear me John."_ He slowly backed himself up the wall until he was standing and began to turn in circles, trying to listen to the voice. "I hear you!" he practically yelled. "Who are you? Where are you?"

"_John."_ He stood still when he heard it. It was not answering his questions. He knew there was nobody else on Atlantis so where was it coming from? Then it hit him like a brick. "Is that you Atlantis? Are you trying to speak to me?"

He received no answer, only silence. The pilot walked over to the wall and placed his right hand on it. He could feel the slight vibration of power but nothing felt new. No extra surge in power to show that she had heard him. Or even if it was Atlantis. He sighed and put his hand back down to his side.

When he turned and saw his friend lying on the ground anger broke out of him. His face contorted in a kind of sneer and then he stormed out of the room. He wasn't going to go into the self pity mode. No way in hell. He was going to find out what was going on and then he was going to get the rest of his crew back. No more crying. He returned to the armory to get more weapons.

* * *

When he finished arming himself again he left and headed towards the generator rooms to see if everything was still operating. Without Rodney he wouldn't be able to know one hundred percent but he would be able to get a very good idea.

Arriving at the first room he saw the small naquada generator sitting there humming along. He checked the connections, saw that everything was still hooked up and then left to go to the second one. When he was finished and satisfied that at least all the generators appeared to be working he headed back to the Control Room to see if he could figure out what happened with the Stargate earlier.

Halfway to his destination he heard the incoming wormhole alarm go off again. "Dammit!" he said and took off running like an Olympic gold medalist. When he reached the room he was out of breath and when he came to the gate room he saw that it was still active. He checked his watch to see how long it had taken him to get there. Less than three minutes. Had to have been a record.

He brought his P-90 up and surveyed the room to see if anybody or anything had come through. When he saw nothing he moved up to the Control Room. Again nothing. Then he slowly moved towards Weir's office and when he got to the door he dropped his weapon in astonishment. His P-90 dangled from its cord which was attached to his tac vest while Sheppard stood and stared.

Ford's body was gone. Not a trace that he had ever been there. No blood, no nothing. Then the Stargate abruptly shut itself down. "All right! Just what the hell is going on here?" he yelled out to no one in particular.

"What do you think is going on Sir?" came the familiar voice again. Sheppard grabbed his weapon and turned around in an instant. He froze when he saw the all too familiar form of Ford standing in front of him again.

"What the hell? Why do I get the distinct impression that I'm being screwed with? I'm mean, this sure isn't deja vu." The pilot said as he aimed his gun at the man.

"What do you mean Sir?" the young man said with a condescending tone as he moved steadily towards the Colonel.

"Just stay where you are Ford." He said as he held his P-90 up even higher. "You're not Ford. I just killed him. And you have no blood on you. So what… the… hell… is going on here? Tell me now before I shoot you."

Aiden's head cocked to the right and a smile broke out on his face. "That's very good Colonel Sheppard. You are starting to figure things out. You are strong and you will be a great vessel indeed."

A light went off in John's head and then an immense feeling of dread overwhelmed him. "Puren?" he said quietly.

The young man clapped his hands together. "Very good Colonel Sheppard. Very good. Yes, I am Puren. And you are now ready for the final process of my take over. You may drop your weapons and prepare yourself."

The dread seemed to dissipate from the Colonel. "Oh, I don't think so Puren. There's no way in hell that you're taking over my body. Not for good. So you can just kiss my ass. You got that?"

"Your weapons are not effective. You cannot harm me in this state." The creature said smugly.

"Yeah well… that's where you're wrong. This is my mind after all. Right?"

"You will not win Colonel Sheppard."

"We'll wait for the verdict on that, won't we?" and with that said he charged the alien.

* * *

"Oh crap!" McKay said. "His vitals are spiking. Something's happening in there."

"What do you mean something's happening Rodney?" Elizabeth said with fear. "Can't you help him at all?"

"It's all in his mind Elizabeth. What can we do from out here except keep an eye on things?"

"Then I'll go in to help him." Came Ronan's raspy voice from behind him.

"Wait. What? What are you talking about?" Rodney said with a mix of confusion and dread. "Are you insane? That's Sheppard's mind we're talking about."

"I know. But there is a second pod and if he's in danger of losing his life I want to go in and help him. I can help him fight."

"He has a point Rodney." Weir said from beside him. "Ronan can use the second pod. I mean, why else would there be two pods hooked up to one control system. It had to be there for backup. In case anything went wrong. It makes sense."

"Okay. But I should be the one to go. I have the technical expertise."

"Exactly Rodney. You have the technical expertise. Which means you should stay here to keep an eye on things. None of us are uniquely qualified to work this equipment. You are. Ronan has the fighting skills that none of us have other than Teyla. So he should be the one to go in and help John."

McKay just stared from Elizabeth to Ronan and then finally conceded. "Fine. But if you come back brain damaged it's not my fault." They all rolled there eyes at the comment and then Carson and the nurses helped Ronan prepare for the pod.

* * *

John landed with a thud up against the main console in the Control Room. He grunted and then slowly stood up. This was all in his head so he should be able to manipulate the pain. Make it go away. But the pain stayed. Which meant only one thing. Puren was in more control of his body than he thought.

They stood and stared at each other for a moment with anger in their eyes and then they both rushed forward at the same instant. When they hit each other they both went down, Sheppard landing on top. He took the sudden change in momentum and managed to get his P-90 up under the alien's throat while he sat on top of him. "It looks like I'm on top Puren." He said with only a bit of confidence.

Seconds later he realized just how wrong that statement had been because he found himself being thrown off the creature. He flew across the room and landed on the floor by the door to Weir's office. He lay stunned, groaning in pain. That had hurt. A lot.

Then he heard laughing. An evil laugh. "I told you that you could not beat me Colonel Sheppard. There is no use in trying. I will have you as a vessel."

"I don't think so." Came a vaguely familiar raspy voice from behind Puren. Sheppard looked up from his vantage point on the floor and was happy to see Ronan standing there with his arms crossed over his chest. He looked pissed.

"Man do I feel sorry for you Puren." And then he put his head back down on the floor.

Seconds later he saw the form of Ford go flying over him and heard the crash as he landed on Weir's desk.

Then he saw a hand come into view. He looked at the Sateden with relief. "Thanks." He said and took the proffered hand. Ronan pulled the Colonel to his feet and then they both turned to look at the alien who was lying in a pile of rubble in Elizabeth's office.

"Having fun." Ronan asked as he took in the fact that Puren looked like Sheppard's old teammate.

"Oh… tones. Can we get the hell out of here now?" he said as he bent over with his hands on his knees. He was breathing heavily and the pain was evident on his face.

Ronan shrugged and they took off running. They knew they still had to kill Puren. But at least there were two of them now and that's what mattered.

**TBC in Chapter Twenty-One….**

* * *

**A/N:** Hope you enjoyed. Did I answer any questions you had? Now that Sheppard knows that Puren was Ford what do you think he'll do to get revenge? I mean the thing let him think that he killed Ford. I'd sure kick his ass. Anyways, ta for now. Later days. :)


	21. Chapter 21

I don't own SGA or any of it's characters. Hey there folks! Sorry this took so long, but I had a death in the family and I really didn't feel like writing anything. This is the first time that I actually felt like writing. So I hope you like the chapter. It's not my most inspiring one and it's a lot of exposition, but hey, it'll do. So, enjoy:)

**Chapter Twenty-One**

"How are they doing Rodney?" Elizabeth asked as she moved up beside the pod which held John.

"They're fine for now. John's vitals have stabilized. And Ronan's… Ronan. He's fine." McKay said.

"How much longer do you think we can keep John in there?" Weir asked.

"It's hard to say for sure, but I say that we have a couple more hours max before there is any real damage. I don't think that it was meant to have someone in there for any extended duration." Rodney said as he pressed a few more keys on his data pad.

"I wonder what's going on in there. How do you think the pods work exactly?"

"I would say that there's a mental aspect to it. He may be dealing with Puren inside his own mind. And if I know Sheppard, he's probably kicking Puren's ass right about now. And Ronan's probably doubled the ass kicking."

"What makes you think that they can fight Puren any better in John's mind than they can in the real world?" Elizabeth asked.

"What can I say, I'm in denial. I can't see them failing at this. I mean come on, it's Sheppard and Ronan. An unbeatable combination don't you think?" Rodney said with his hands on his hips.

"Let's hope so Rodney." Weir said as she looked down at Sheppard. "Let's hope so."

* * *

"Sheppard. We can't stay in here forever." Ronan said as he kept watch at the entrance to the infirmary.

"I know that Ronan." John said with frustration evident in his voice, along with a bit of pain. "I'm just trying to catch my breath and think up some strategy. I get this is all in my head and all, but man, I feel beaten down."

"Hmm." Ronan said as he turned to face him and raised his left eyebrow.

"This sucks. I feel old. I wonder how my body is taking this out in the real world. I'd hate to think that anything that happens to me in here happens to me out there too. That would be just too Matrix-esque if you ask me. Welcome to the real world Neo."

Ronan just stared at him with confusion, not getting the pop culture reference. "Is that another Earth saying?"

"Something like that Ronan. Yeah. You know when this is all over and Puren's dead and gone, you're going to have to sit down and watch all three Matrix movies with me. I think you'll like them. There's a lot of kick-ass action in them."

"Okay." Was the only answer that John received before Ronan turned back to face the entrance.

Sheppard shook his head, sighed and then stood up from the chair he was sitting in. He had a lot to teach the Satedan. "So, it's been ten minutes since we ran off from Puren." He said as he looked at his watch and then moved forward to stand beside his companion. "At least I think it's been ten minutes. It could be twenty for all I know. This is my brain we're talking about and time can be a hard concept for me sometimes. Just ask Elizabeth. She has plenty to say on that subject." John crossed his arms in front of him and looked down the hall in front of him.

"Do we have a plan yet?" Ronan asked without taking his eyes from the doorway.

"Let's just say there are ideas percolating in here," He said pointing to his head. "And leave it at that for the moment."

"You're usually a lot quicker at coming up with a plan Sheppard."

"I know. I know. I have a feeling that Puren is partly to blame for that. Things just seem sluggish at the moment. Dammit! I think he's moving a lot quicker through my mind now. He doesn't know what we're doing here but he's going to figure it out eventually. We have to come up with something soon or I'm going to be toast. And I'm sorry, but I like my brain just the way it is thank you very much. I don't need a self involved egomaniac setting up shop in here."

"I say we try and trick him." The Runner said.

John turned to face the man. "In what way?" he asked curiously.

"We make him think that he's taken you over and when the time comes that he's all full of himself and has let down his guard we strike out and kill him."

Sheppard cocked his head and thought about that statement for a moment. "I like it, but how are we supposed to trick him into thinking he's taken me over. He'd have to know that I'm holding out on him."

Ronan grinned. John blinked with wide eyes at the rare occasion of seeing the taciturn man smile. "What?" he said, smiling back.

"I leave your mind for a moment and speak to McKay. Get him to set something up from the outside. Something that Puren has no idea about. Then I come back in, tell you what he's doing and then we set the plan in motion."

John's smile broadened. "You know Ronan. You really are a lot smarter than people give you credit for."

"That was a compliment, right?"

"Definitely. I think you'd almost give McKay a run for his money. But don't tell him I said that. Because that's all I need. Hearing him complain that I must be brain damaged to think that way."

Ronan thought about that for a moment, grunted his agreement and then closed his eyes. Within seconds he had disappeared from view.

"So that's how that works. Cool. And I guess I'll see you shortly Ronan. Thanks for saying goodbye. I'll be waiting here for you as long as Mr. I'm-Better-Than-You doesn't show up wanting another fight." He moved away from the entrance slightly and leaned against the wall. He hoped he didn't have to wait that long for Ronan to get back because he had to admit that he was a little freaked out being in this situation alone. And it didn't matter that all of this was in his mind. He just knew that he couldn't do this alone. And he knew that if this plan didn't work he would probably be dead. 'Dammit!' he thought. 'How the hell do I get myself into these situations?'

* * *

Ronan's eyes opened and the pod slid out from the wall. He immediately sat up and turned to face the people in the room.

"What are you doing back out here?" Rodney asked before anyone else could. "You're supposed to be helping Sheppard!"

"I am helping Sheppard McKay!" he said and stood up in front of the scientist.

"How could you possibly be helping him from out here? I thought the whole idea was that you were going in for muscle. To help him fight Puren."

"Just let him speak Rodney." Weir said as she moved up beside the Runner, along with Teyla and Carson.

"We came up with a plan. We're going to trick Puren into thinking that he's taken over Sheppard."

"What good will that do from out here?" Rodney broke in before Ronan could finish. The Runner gave a low growl at the man and McKay shut up.

"I came out here to talk to you McKay. To see if you can do anything from out here to help with the deception. We need to make it look real enough that Puren will let down his guard. And when he does we can kill him."

Rodney thought about it for a moment. A long moment.

"Well?" Weir asked. "Is it possible or not?"

"I think it may be. Yes." Rodney said and then turned back to his data pad. "Let me see what I can come up with."

"Be as fast as you can McKay." Ronan said with a frown. "I can't leave Sheppard alone in there for very long or Puren will find him and come after him. I want to be there to help him. And I can't do that until I get your side of the plan."

"Yes. Yes. I'll hurry. Now leave me alone for a minute so I can think."

The group slowly moved away from the scientist and walked over to where Sheppard lay in his pod.

"Do you think this will work?" Elizabeth asked Ronan.

"It better. It's my idea." The man said gruffly and then crossed his arms in front of him.

"Your idea?" she asked surprised. "John must be having a harder time in there than we thought. He's usually pretty quick at coming up with ideas."

"I know. I said the same thing to him. He thinks Puren is partly to blame."

They all sighed and looked at Sheppard. They were all thinking the same thing. 'Is this going to work?'

* * *

Sheppard stood near the entrance to the infirmary with his P-90 ready to go in front of him. He knew that none of this was real, per se, but he also knew that he could still get hurt. A lot apparently.

It had felt like Ronan had been gone for a long time. In fact, he really had no concept of time. It was just a gut feeling at this point. He didn't know how much longer he would have to wait or if Puren would show up in the mean time. He really preferred for Ronan to be by his side if that happened. He didn't want to fight the alien alone.

He was getting bored and tired. And there was only so much waiting he could do. Then, as soon as the thought had left his mind he heard familiar voice. Extremely close by. "Colonel John Sheppard. Did you not think that I could find you?"

John jerked and when he turned around Puren was standing not two feet from him. Then he felt a hard blow to his face as Puren threw out his arm and hit him. The Colonel went flying backwards and hit the wall. When he landed on the floor he let out a pained breath and then spit some blood out of his mouth. He lay on his stomach and he pulled his arms slowly underneath him so that he could try and push himself up. It hurt like hell.

"Where did your bodyguard go? Has he left you to fend for yourself? All the better for me Colonel John Sheppard." The form of Aiden ford said to him with a malicious grin on his young face.

"Oh he hasn't gone far you bastard." John said slightly out of breath.

"Then where is he? Hm?"

"Wouldn't you like to know." The pilot said as he began to push himself off of the floor.

"Yes I would. And you're going to tell me." Puren said, moving closer.

"Not bloody likely."

"I can be quite persuasive when I have to be."

"I'm sure you can. But you're not going to find out." Sheppard said as he managed to get to his knees.

Puren came up to stand over the soldier. He reached down and took hold of John's left hand. Then the next thing Sheppard knew, he was feeling white hot pain erupt from his index finger. He yelled out and looked up at the large smile on Aiden's face. Another broken bone he thought around the pain. Another broken bone.

* * *

They all turned in a hurry when they heard Sheppard yell out from within the pod. Rodney immediately checked the man's vitals on his data pad.

"What the hell is going on in there?" Elizabeth asked as she ran over to the pod and placed her hand on the glass.

"His EEG just majorly fluctuated. He's in a lot of pain. I couldn't say what happened though." McKay said quickly.

"I need to get in there now." Ronan said angrily. "Puren has to have found him. So do you have anything I can use or not?"

"Give me two more minutes and I will!" Rodney said brusquely.

"He doesn't have two minutes McKay!" Ronan said a little louder.

"Yelling at me isn't going to get it done any faster. Do you want this or not?"

Ronan turned to face Sheppard and tapped his foot impatiently. He hated not being there to help. He had left the man there alone and now he was paying for it. They were both paying for it. He hoped that by the time he did get back in to Sheppard's mind that the man wouldn't be dead.

**TBC in Chapter Twenty-Two….**

* * *

**A/N:** Well, I hope you liked the chapter. I don't know when the next time is that I will write. Maybe friday night or maybe on the weekend. I will try to write a couple more chapters before I go on vacation. I don't have a computer to use where I'm going, so if I go for another long period of time without submitting anything, don't worry. I'm just on vacation. So TTFN. Later days. :)


	22. Chapter 22

I don't own Stargate Atlantis or any of its characters. My bad guy is my own though. Hey there folks. Holy crap it's been a really long time. I think I just went into writer's block mode with this story. And I also dedicated most of my down time to writing a couple of completely home made stories with all of my own characters. Absolutely nothing to do with fan-fic. I wish I could post those stories because I love them. They have the same main character and he's awesome. Oh well, I hope you enjoy this chapter. It's not really the best but bear with me, I'm getting back into the swing of things. And I tweaked the rest of the story to make it even better. There probably won't be a whole lot left, but we'll see. Ta for now. :)

**Chapter Twenty-Two**

Sheppard lay on the floor with his hand cradled against his stomach. All he could feel was the pain. His eyes were closed and his teeth were clenched tight. He tried to think of Ronan but his brain wouldn't let him. It was all about the pain. Then his eyes flew open when he heard the whispering voice again. _"Ronan's coming back John. Don't worry. He's coming." _He now knew exactly who that voice belonged to.

He looked up at the imposing form of Puren standing over him in Ford's body. The evil sneer had not left his face. He knew that both he and Ronan were going to wipe that smile off of his face. He wasn't about to let the bastard win. Not in his own brain godammit! Not ever.

"You know," John said with his teeth still clenched "You are one dead motherfu…."

"Now, now Colonel John Sheppard. There is no need for such language. Is it really necessary?"

"Yes it is. Totally necessary. I only wish I weren't saying it to Ford's face. Cause that's something that I would never say to him."

"Then maybe I will change into a different form. How about this one? Does this suit you better?" Puren's image fluctuated and then he became another person.

John just stared at him, trying to ignore the pain the best that he could. "I don't believe you. You are such an asshole."

"What? You do not like this image?"

"I would like it better if it wasn't someone who was already dead." He said angrily. "I don't need to rehash those feelings thank you very much. Why don't you just show me your real image? Or are you just too afraid to do that?"

"This is more fun John Sheppard. Why would I show you my real self when I like these images better? And before we completely get off of the subject, you are supposed to be telling me where your bodyguard went to."

"I told you that wasn't going to happen. No amount of torture is going to get that answer out of me. So go screw yourself Puren." John tried to smile but it just came out as a grimace instead.

An angry look crossed Puren's face and he move towards the Colonel again. He reached down and grabbed hold of his hand again. He yanked it up as John protested. He yelled out in pain again as the finger next to the already broken one erupted in white hot pain. Now he had two broken fingers.

"You will answer my questions."

Everyone in the lab jumped when they heard Sheppard yell out a second time. They turned to look at him and saw that he was still unconscious. They knew he was in tremendous pain.

"McKay!" Ronan said emphatically.

"Almost have it. Almost have it." The man said hurriedly.

"Now McKay! He's hurting Sheppard!" Ronan said as he moved closer to the man. He practically stood in his space to make him work faster.

"Okay…. Done! Now here's the plan."

* * *

Sheppard now lay on his back, holding his hand to his chest. Tears were streaming down his cheeks to the floor. With two broken fingers on the same hand all that entered into his mind was the pain. He could feel himself going numb. He stared at the ceiling and a stray thought of Ronan popped into his head. He prayed the man would come back. Then it was gone and the numbness overtook him.

Just as Puren was about to grab for John's hand again Ronan appeared behind him and grabbed hold of his shoulder. He threw him backwards and watched as he landed with a thud on the floor near one of the gurneys. Ronan turned back, bent down and took hold of Sheppard by his torso. He put one hand on either side and pulled him to his feet. He put the man over his shoulders and headed off to find a safer place.

Puren lay stunned on the floor of the infirmary.

* * *

A short time later Ronan sat beside the bed that Colonel Sheppard lay on and wrapped his injured hand with gauze from a first aid kit. The man was fading. Ronan knew the pain must have been overwhelming. He tried to speak to his friend. "Sheppard? Can you hear me? Are you there?"

There was a slight nod from the man, otherwise there was no response. Ronan finished wrapping the hand and then carefully placed it on John's stomach. He knew he had McKay's plan, but how were they supposed to carry it out if John could barely function? He couldn't do it by himself. The plan hinged on Sheppard being able to trick Puren into thinking he'd won. It wouldn't work with just him.

Ronan stood up and walked around the quarters they were in. He didn't know who's they were, but it was a sparse room. A few pictures in frames by the bed and a guitar in the corner by the window. He didn't think he knew this particular crew member. He thought it had to have been somebody new who had come over on the Deadelus. He rubbed his face with his hands and then looked back at Sheppard. He didn't know how to get Sheppard back into the plan.

* * *

"Something must be wrong. Nothing's happened yet." Rodney said as he turned to look at the pods where John and Ronan were.

"Maybe you have to give them a little time." Weir said with some hope.

"No that's not it. You heard me tell Ronan that he had to give me ten minutes and then they could act. It's been over that and nothing's happened yet. Maybe Sheppard was worse off than we thought. It did sound like he was in a fair amount of pain. If they don't start anything soon then this plan won't work."

Teyla walked over to the pods and placed one hand on each. She closed her eyes and began to pray. Then she spoke quietly. The others could barely hear her. Then they all walked over to her and stood around the pods. Praying together.

* * *

Ronan was sitting beside the Colonel when he could hear whispering around him. He looked around but saw nothing. Then he heard it again_. "Ronan. Please, you must put your plan into action. You must. Time is running out." _He wasn't sure he heard it at first, but then he knew that it was Teyla. Sheppard had mentioned something about hearing Elizabeth's voice. Now he was hearing Teyla's. Letting him know what he had to do. Then he heard more whispering. Many voices this time. _"We're praying for you."_ That was Becket. _"We're all here for you and John."_ That was Weir. _"Come on buddy. Get your buts in gear."_ And that was McKay's contribution. Ronan sighed and then stood up. They were right. He had to act. Both of them did.

"Come on Sheppard. This is all in your head. Literally." He said as he reached down and shook the man lightly. "Get with it. If this is in your head then you should be able to do what you want. Don't let Puren take control. Fix your hand, get rid of the pain, put the plan in motion." He shook a little harder.

John's eyes opened and he looked at the Runner. Ronan looked back at him. After several seconds John brought his hand up in front of him and then closed his eyes again. "What are you doing Sheppard?" Ronan asked as he took his hands off of the pilot's shoulders and then stood back.

John opened his eyes again and looked at his friend. "I'm doing what you told me to do Ronan. I'm doing what I want. He grabbed hold of the gauze with his other hand and began to unwrap it. When he finished Ronan just stared at the hand. John flexed his fingers and sighed. "Man, I wish that I had been able to do that sooner. Thanks buddy. Thanks a bunch."

"What took you so long?"

"I guess I need the motivation. Let's say we go kick some ass and get this bastard out of my noggin. Huh?" John smirked.

Ronan smirked back and then he helped John sit up. "I couldn't agree with you more Sheppard."

They left the room at a dead run, both smiling the whole way.

**TBC in Chapter Twenty-Three….**

* * *

**A/N: **Hope ya'll enjoyed the first chapter I've written in a while. So what do ya think? Is Puren going to get his ass kicked finally? You just wait and see my friends. Later days. I should be able to finish this soon. I hope. Now I'm off to listen to the thunderstorm. I don't know how relaxing that will be at 10:30 at night. Not really what's going to help me get to sleep. Have fun!


	23. Chapter 23

I don't own SGA or any of its characters. Puren is all mine though.

Howdy folks. I have actually written another chapter. Yay! I didn't think that it would happen so soon. But I've had it on the brain all day so I did it. And it looks the plan is afoot. Hope you enjoy because this is winding down. Ta. :)

**Chapter Twenty-Three**

"Do you think that Ronan heard us?" Weir asked as she leaned against the wall between the two pods. She had her arms crossed in front of her. They had been waiting for almost fifteen minutes for something to happen. They were getting anxious as well as bored. Not the best combination for the group.

Rodney looked up at Weir from where he was sitting by the console. He looked tired. "I would say he did hear us. He did mention that Sheppard had talked about hearing whispering around him. That had to have been us. I just don't get what's taking so long. Something has to have gone wrong."

"Isn't there anything else that we can do Rodney?" she asked with an imploring look on her face.

"I'm sorry Elizabeth. I've done everything that I can up to this point. I gave Ronan the plan and told him to give me ten minutes to do what I had to do from here. After that it was up to him and Sheppard. Maybe Sheppard was in no condition to help. That's always a possibility." He looked over at the pods and sighed.

Weir sighed as well and looked at the remaining people in the lab. Teyla was sitting against the far wall with her knees up to her chest and her arms folded across her knees. She had her chin on her arms and seemed to be staring at some point on the floor. She looked extremely tired and the boredom was showing. She then turned her head and looked at Becket who was sitting on the gurney that was against the wall to her right. His legs were dangling over the edge and he had a hand on either side of him, resting on the bed. He was looking at the two of them, listening to the conversation. She cocked her head and smiled wanly at the man. "Do you think they'll be okay Carson? Like Rodney said, something must have gone wrong."

"It's hard to say Elizabeth. I'm not sure what damage the Colonel will have with everything that has happened in the last few days. Both physical and mental. And I really want to see why he yelled out the way that he did. Ronan is another story. He seemed to be okay when he came out the first time, but we don't know what's going on in there. Something could happen to him while inside the Colonel's mind. And it may show on him physically out here. We'll just have to wait and see. Sorry I can't give you more of an answer."

She smiled at him again and then looked back at McKay. "You're absolutely sure that there's nothing else that we can do? I just hate sitting around here doing nothing. I just doesn't feel right."

Rodney shook his head. "I'm sure there nothing we can do. We just have to wait and see if Ronan and Sheppard are able to start the plan. I'm sure we'll be able to figure out if something is happening just by watching their EEGs. Or the control panel for that matter. Something has to happen soon. You'll see Elizabeth."

They all sighed collectively except for Teyla who had not entered into the conversation. She had just continued to stare at the floor. Nobody decided to interrupt her boredom.

* * *

John and Ronan had made it safely to the armory again and had systematically gone through everything to see what they could use. In the end Ronan grabbed a couple of flash bangs and put them with his stunner. He really didn't seem to think that he needed anything more. Sheppard on the other hand felt that he needed more fire power. Even though they were setting a trap he didn't want to go into the situation unarmed. He knew that he would feel naked. So to speak. Plus, it was his mind and he could use as much weaponry as he felt he needed. He would use an A-Bomb to blow the sucker up if he thought it would do any good. The pilot stuck a service revolver in its holster at his hip and then armed his P-90. He stuck some extra clips into his tactical vest and then fixed the position of his radio. Then he checked the com in his ear. Everything was in working order. But then again, it was his brain, so why wouldn't everything be working? He just hoped to god that their plan would work because he really didn't want the roommate in his head anymore.

Ronan and John stood for a couple of extra moments to do one final check on their supplies and then they nodded at each other. Words were not necessary when they knew exactly what they were going to do. They headed out the door and then went in separate directions. Their plan was in motion. And they both thought as they headed down their respective hallways, 'I better not die.' If they only knew how alike they really were. They would probably laugh.

* * *

John came around a corner and pointed his P-90 out in front of him. He was headed towards the infirmary. The last know place where Puren was. If he didn't find him there then he had a pretty good idea where he was. John thought about it for a moment as he stealthily moved along. 'Why the hell do I keep calling it him? –It- is more like it. It's an Ancient device that thinks it's alive.' The thought continued as he made his way down the next hall. He stopped when he reached the infirmary.

He peered around the corner and saw nothing. He moved a little farther inside and scanned the area. Still nothing. When he had decided that Puren was no longer there he turned and left the room. He tapped the com in his ear. "Hey Ronan." He spoke quietly. "Puren's not in the infirmary. I'm heading to the Control Room."

"I haven't been able to find him either." Came Ronan's tinny voice over the com. "I'll follow your lead and meet you there."

"See you in five." And he tapped his earpiece again. John slowly made his way to the nearest transporter and stepped inside. Within seconds he was on the level that he wanted. Minutes later he spotted Ronan coming from the opposite direction and rendezvoused with him. "He has to be here because he doesn't seem to be anyplace else." John said quietly.

"I'll check around the Gate." Ronan said matter of factly.

"I guess that means I'm checking the Control Room. I'll signal you if I spot him. You do the same." Ronan nodded at him and he began to move away. "You know, he could be watching our every move." John said in his own matter of fact tone.

Ronan turned to face him. "I know." He said and then left the room.

Sheppard watched his back as he left, smirked slightly and then head to the Control Room. Again he hoped the plan would work.

* * *

After Sheppard did a quick search of the Control Room he walked to Weir's office and before he could reach the room he knew what he would find. He could just make out that somebody was sitting in her chair. He looked through the glass and sure enough the form of Ford was sitting in her chair with his feet up on the desk, crossed at the ankles and his hands were crossed behind his head. When John reached the entrance he could see the look on Puren's face. It was satisfaction.

"I am glad to see that you have finally arrived Colonel John Sheppard. I was beginning to think that you would not grace me with your presence." The look turned evil as put his feet down and sat forward, clasping his hands together in front of him on the desk. "I guess that I was wrong."

"Yeah. You were wrong. This is my brain and you're not going to screw with it. Not any more. I've seen the error of my ways and you're going to get your butt kicked. I can guarantee you that."

"Such optimism. I like that in a vessel. It just makes things more enjoyable. You can not win John Sheppard. I thought that you would know that by now. I guess that I will have to give you more pain before you get it into your head. I am the Supreme. I will have your soul and I will win. Do not deny me."

A slight flicker of panic appeared on John's face and then an instant later it was gone. Puren didn't notice. They stared at each other for what seemed like an eternity, the whole time Sheppard was wondering how he was going to let Ronan know that he had found their adversary. Then John decided to stop the staring contest and raised his P-90. He aimed it at the Ford wannabe and put his finger on the trigger. 'The plan will work.' He thought an instant before Puren attacked.

**TBC in Chapter Twenty-Four….**

* * *

**A/N:** Hope you liked cause I've been sitting here, for like an hour, trying to think of what to write. And I left you hanging. So sorry. And holly crap, I feel like I'm dyslexic with this damn keyboard. It's taking me twice as long to type because I keep having to delete all the mistakes I'm making. I know what I want to say but words keep coming out all mixed up. Ahhhh!! I feel like ripping out my hair I'm so frustrated. Anyways, thanks for the reviews on the updates. Sooo welcome. Please send more. Later days guys. :)


	24. Chapter 24

I don't own SGA or any of its characters. Puren, however, is mine.

Well, here ya go. Here's another chapter and it's a doozy. I just came up with this idea on the way home from work and I love it. I knew that I would have to figure out what their plan was. I kept mentioning it and now I actually had to show it. So here you go folks. Hope you enjoy because I had fun writing it. :)

**Chapter Twenty-Four**

John fired his weapon and realized too late that Puren had the upper hand. The P-90 was swatted out of his hand and he landed flat on his back, Puren on top of him. He was grabbed by the throat and he began to choke. "You… can't… kill… me." He said between breaths. He was beginning to see black spots in front of his eyes. That wasn't a good thing.

"Who said that I am going to kill you John Sheppard. That is not my intention. Why would I kill my vessel?" he smiled evilly at the pilot and then lifted him up by the neck. "This will work even if you are unconscious."

John tried to push him away but couldn't get any kind of grip on him. His hands fumbled as he tried to make them work. Then his feet involuntarily flailed when he found he was no longer touching the ground. 'The plan isn't going to work.' He thought just before he blacked out.

Puren smiled and then placed the Colonel on the floor of the office. He looked around, wondering why the bodyguard had not shown up yet. He knew that he was around somewhere. He had seen him talking to Sheppard. Puren slowly walked around John until he was standing by the top of his head and then reached down, grabbing both of his shoulders. He pulled him up and slid him around to the couch that sat off to the side of Weir's office. He lifted the man and practically threw him on it. Then he maneuvered him around until he was laying on his back. The moment felt so right. Soon he would have a worthy vessel and nobody could stop him. He would live forever. The way the Supreme was meant to live. He sighed and bent over the Colonel's face. A feeling of absolute joy filled him. Then he opened the Colonel's mouth and prepared to take the 'soul'.

* * *

Rodney jumped to his feet when he heard the beeping coming from the console behind him. Nobody in the room could tell whether he was scared or happy. They figured a bit of both. "It's working!" he said excitedly. "It's working! I can't believe it! Holy crap, this just may work after all!"

Weir came running up to his right side and both Teyla and Becket stood on the other side of the console. "They've started?" Weir asked and then turned back to look at John and Ronan, still in their pods.

"Finally! Yes they have. It's about damn time. I was beginning to think that it wouldn't work. That something had happened to Sheppard and we wouldn't get him back. We'll have to ask them what took so long. I mean come on, half an hour. It felt like it was five hours. I'll kill them if they end up dead!"

The others just stood and listened to the man rant, knowing that they felt the same way. They were happy that something was finally happening. That soon they just may get their Military Commander back.

Rodney reached over and picked his data pad up off of the console and pressed a few buttons, then he checked the connection to the Ancient machinery and pressed a few more buttons. "Everything looks good. Their EEGs are within norms, no spiking that I can see. And the sub routine is running smoothly." He looked up at the others. "All looks good guys."

Elizabeth, Teyla and Carson all sighed with relief simultaneously and then walked over to the pods. "Be safe." Elizabeth said to both her men and then reached out and grabbed hold of Teyla's hands over the top of John's pod. They smiled at each other, both happy that their friends were going to make it. They knew it in the bottom of their hearts. This would be over soon.

* * *

Ronan heard the yelling from Weir's office and took off running up the back entrance to the Control Room. He didn't want to let Puren see him. When he finally reached the opposite end of the Control Room he peered around the corner and saw that Puren was on top of Sheppard. Then he saw him lift John up by the throat. Things were going according to plan. Not the choking part, Ronan knew. But that was an added bonus to let Puren think that he was winning. He wondered what Sheppard was thinking of right at that moment. Probably that the plan wasn't working. But he knew deep down that it was. That they would be out of Sheppard's mind soon and back in the real world. He smiled slightly and then turned and headed back down towards the Gate.

* * *

Puren slowly began to suck out John's 'soul'. He had his mouth inches from the pilot's mouth, not touching it. Mist seemed to rise out of Sheppard's open mouth and went into the fluctuating form of Ford. Puren's whole body seemed to be vibrating, completely enjoying the moment. It took several minutes and then finally he let go of John's mouth and stood up. He had his eyes closed and he was breathing heavily. If anybody else had seen him at that moment they would have thought that he was stoned or drunk. He was high on the 'soul' of Colonel John Sheppard.

He staggered back and almost bumped into Weir's desk. Then he moved around and sat down in her chair. He now had a vessel. Finally after all the millennia that he had been stuck in that cave. He now had a vessel and he could move around freely. And nobody would be able to stop him. He was SUPREME!

Puren looked over at the spent body of Sheppard and smiled. Now all he had to do was get rid of the interloper of a bodyguard. But now that he was all powerful that would be now problem. He decided that for now he would keep the form of Aiden Ford. Just until he got rid of Ronan Dex. Then he would become his full self. Just wait until they saw what he could do. Everyone would bow in awe.

* * *

The console beeped again and McKay picked up his data pad. "Hmm." He said non-chalantly and then pressed a few buttons. He looked at the console, pressed a few buttons there and then went back to his data pad. He nodded his head slightly and then said "Hmm." again.

"What is it Rodney? What's going on?" Weir asked as she came up behind him. "Is it anything important?"

Without turning around Rodney spoke up. "Don't worry Elizabeth. Everything is going smoothly. It was just telling me that the second part of the plan was in motion. We're good."

Elizabeth sighed and looked back at Teyla and Carson. She shrugged her shoulders and then walked back over to stand with them. They were all getting antsy. They wanted this to be over and done with. She patted her friends on the shoulder and then smiled wanly. She hoped it would be over soon.

* * *

Puren strode confidently down the halls of Atlantis looking for Ronan. He had no worries that the man would be able to hurt him. He would kill this Ronan which in turn would kill the Ronan in the real world. It was only a matter of time before he found the man.

"Come out, come out wherever you are Ronan Dex!" he yelled out as he walked. "There is no point in hiding any more! I have defeated John Sheppard and have taken over this mind! You are no longer welcome in here! I will find you eventually!" He continued to yell out as he moved.

When he came full circle and ended up back at the Control Room he decided that he would check out the Gate Room. He walked down the lighted stairs and stood out in the middle of the opening. As he looked up at the Gate he couldn't help but marvel at the structure. He knew that he would be able to move at will through as many as he wished. Would be able to spread the word of the Supreme to other worlds. Soon, very soon that would be his destiny.

"I am waiting for you Ronan Dex!" he yelled out, knowing very well that the man was listening to him. Probably circling his position at that very moment. "Why hide Ronan Dex? It is inevitable that you are going to die! So why make this harder than it should be? Why don't you just come out and face me?"

"Because. Then I wouldn't get my chance to kick your ass!" came a familiar voice from up above. Puren's heart jumped up into his throat and he turned as fast as he could and looked up to the balcony which overlooked the Gate Room. What he saw almost made him drop to his knees. 'This isn't possible.' He thought as he stared at the person that stood above him. Puren's eyes were as wide as saucers.

**TBC in Chapter Twenty-Five….**

* * *

**A/N:** So, how did you like it? Do you know who yelled back at Puren? Have you guessed? You're going to have to wait until the next chapter to find out. Oh well. But don't worry, I'm on a roll. So I may be posting again tonight. If not, then tomorrow night. Ta for now. :)


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